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citations from http://www.ingentaconnect.com/

2007-04-01
2013-05-28
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  • Nobody/Anonymous

    Hi Matthias,
    the export function for ingentaconnect offer two citianon export funtions:
        * EndNote
        * BibTEX

    both are not working.
    Maybe you know why and are albe to implement or improve this.

    With regards Knut

     
    • Matthias Steffens

      Hi Knut,

      I just tried the export formats from IngentaConnect. In case of BibTeX, their first line has a space between the record type identifier ("@article") and the succeeding brace ("{"). Also, their BibTeX cite key (which follows thereafter) contains spaces. Is this allowed?

      If you remove all spaces in the first line of their BibTeX exports, then refbase should be able to import them fine. As an example, convert this line:

      @article {Vanella:March 2007:0722-4060:449,

      into this:

      @article{Vanella:March2007:0722-4060:449,

      W.r.t their Endote (RIS) records, you have to remove the first four lines:

      Provider: Ingenta
      Database: IngentaConnect
      Content: application/x-research-info-systems

      i.e., copy everything starting with (and including) the "ER  - " line into the refbase import form, then it should work.

      Btw, their RIS exporter is pretty much broken. In addition to the above issue, they put the "ER  - " tag at the beginning of the record (but it should be at the *end* of the record). Also export of accented characters fails miserably, and author names that contain accented characters will get split into several AU pieces!

      Frankly, I can't understand how big database providers such as IngentaConnect can't even get this simple stuff right. The quality of citation output from major database providers tends to be very poor (Springer is not any different), which is somewhat frustrating.

      Matthias

       
    • Nobody/Anonymous

      Hi Matthias,
      seems that there are different problems:
      have alok at:
      http://www.ingentaconnect.com/content/tandf/ttie/2005/00000006/00000001/art00002

      Regards Knut

       
    • Nobody/Anonymous

      Hi Matthias,
      sorry for the questions.
      The admin of the wwebserver told me to include the Bibutils to the script directory.
      Due security issues there is no safe_mode_exec_dir  definded.
      I did not find the answers in the troubleshooting page ...
      Therefore I used the described SQL command to change Bibutils path.
      1. Questinon
      is this a solution?
      2. question?
      how could I recognise whether the sql command was proceded correct?
      3. Question
      Do you mean the full absloute Server path or the
      path from the root directory of the URL?
      4. Question
      how could I test the Bibtex installation without console access?

      Regards Knut

       
      • Matthias Steffens

        Hi Knut,

        am I understanding you correctly that you're refbase installation is located on a shared server, i.e. you have no root access to the server, and no command line access?

        > The admin of the wwebserver told me to include the Bibutils to the script
        > directory.

        So the Bibutils executables do exist on your server? Can you see the Bibutils utilities within your script directory when being logged in to your server account?

        Do you know the full path to this script directory? By "full path" I mean the full server path. As an example, the path to this script directory could look like this:

        /var/www/my_user_account_name/bin/

        > Due security issues there is no safe_mode_exec_dir  definded.

        Does this mean that PHP 'safe_mode' is turned ON on your server? This is an important information. If yes, then the only way to get Bibutils running will be to put Bibutils into the directory specified in 'safe_mode_exec_dir'. You'll probably have to talk to your admin about this.

        A first check would be to test Bibutils directly on the server's command line (i.e. not via refbase). But if you're on a shared host, this is probably no option.

        > I did not find the answers in the troubleshooting page ...

        W.r.t. Bibutils, here's a bit of troubleshooting information:

        <http://wiki.refbase.net/index.php/Installation-Troubleshooting#Export_of_records_results_in_a_blank_page>

        > Therefore I used the described SQL command to change Bibutils path.

        That's good. So you can execute MySQL commands on your server (via tools such as phpMyAdmin)?

        Using the example path from above, your SQL query should look similar to this:

        UPDATE depends SET depends_path = "/var/www/my_user_account_name/bin/" WHERE depends_external = "bibutils";

        > is this a solution?

        It's part of the solution. The above linked wiki page lists other required parts of the solution.

        > how could I recognise whether the sql command was proceded correct?

        Even if you've entered the correct path, import/export of Endnote & BibTeX records may still fail, since *all* the requirements outlined on the above linked page must be fulfilled.

        Especially note that if you're on a shared host, a special temp directory may have been given to you. If you don't know the path to your server account's temp directory, then you'll need to talk to your admin about this.

        As an example, your temp directory path might look like this:

        /var/www/my_user_account_name/phptmp

        Try to enter this path as value of the '$tempDirPath' variable in file 'includes/execute.inc.php' (line 154, in function 'getTempDirPath()'). We should probably provide a variable in 'ini.inc.php' for this since it seems to be a constant issue for many people.

        > Do you mean the full absloute Server path or the
        > path from the root directory of the URL?

        The full absolute server path (see above).

        > how could I test the Bibtex installation without console access?

        I assume you meant Bibutils installation? Without access to a command line, it will be hard to test. You may want to point your admin to the above linked wiki page and ask him about the points listed there. In short, Bibutils must be accessible by PHP (safe_mode? correct permissions?) and by refbase (full server path in table 'depends'). In addition, Bibutils must be able to write files to a temp directory.

        Btw, the Bibutils developer (Chris Putnam) has recently restructured Bibutils to function as a library (it's written in C, though). I don't know enough about it, but there may be a way in the future to work around the command line requirement, which would help users a lot getting Bibutils running with their refbase installation.

        I hope this helps,

        Matthias

         
    • Knut Krüger

      Knut Krüger - 2007-04-03

      Hi matthias,
      I will answer partially just at this time:
      >am I understanding you correctly that you're refbase installation is located on a shared server, i.e. you have no root access to the >server, and no command line access?
      Yes

      >So the Bibutils executables do exist on your server? Can you see the Bibutils utilities within your script directory when being logged >in to your server account? 
      There are 13 files bib2xml,copac2xml,end2xml ....xml2bib,...,xml2word I hope these are the executable files.found them at the bibutils site. Its a LINUX Server

      >Does this mean that PHP 'safe_mode' is turned ON on your server? This is an important information. If yes, then the only way to get >Bibutils running will be to put Bibutils into the directory specified in 'safe_mode_exec_dir'. You'll probably have to talk to your >admin about this.

      I talked with the Server Admin and he told me that there is a possbility to execute the files outside the safe_mode_exec_dir.
      The files must be located in the same directory as the script. The option to change or to install the safe_mode_exec_dir is disabled and safemode is turned on. He told me that it is normally not necessary to use this feature.
      Hope he is right.

      >> Therefore I used the described SQL command to change Bibutils path.

      >That's good. So you can execute MySQL commands on your server (via tools such as phpMyAdmin)?
      By the way. There was no chance to setup the database with the install script.
      I did the first setup with the SQL file in PHPMyAdmin.

      the path is stored in the database as shown (with my values) on the Trouble shooting page

      There are several files in the PHPtmp directory, but with the attributes 600 this is another problem.
      I am not able to delete the files and it seems that refdb ist writing the session infos (login) without deleting them.

      But this shows that the Phptmp path is usable.

      ------------- additional information if necessaray move to another tread-------------------

      But there is another error during uploading files, maybe there is hint for anything wrong installation:
      Its an PHP Version 4.3.11

      Warning: preg_replace(): Unknown modifier '\' in /home/www/web25/html/uni/refdb/includes/include.inc.php on line 3631

      Warning: preg_replace(): Unknown modifier '\' in /home/www/web25/html/uni/refdb/includes/include.inc.php on line 3634

      Warning: move_uploaded_file( /home/www/web25/files/63_A.DouglasWilson2006.pdf): failed to open stream: No such file or directory in /home/www/web25/html/uni/refdb/modify.php on line 1169

      Warning: move_uploaded_file(): Unable to move '/home/www/web25/phptmp/phprzqfX4' to ' /home/www/web25/files/63_A.DouglasWilson2006.pdf' in /home/www/web25/html/uni/refdb/modify.php on line 1169

      Warning: Cannot modify header information - headers already sent by (output started at /home/www/web25/html/uni/refdb/includes/include.inc.php:3631) in /home/www/web25/html/uni/refdb/modify.php on line 1046

      and another hint: The PFD icon is visible after this corrupted upload and the filename is in the files field.
      but there is not file in the directory.

      Sorry for the problems Knut

       
    • Matthias Steffens

      > There are 13 files bib2xml,copac2xml,end2xml ....xml2bib,...,xml2word I hope
      > these are the executable files.found them at the bibutils site. Its a LINUX
      > Server

      If you've downloaded those Bibutils executables that match your server's platform, then you should be fine. However, permissions must be set correctly for the Bibutils executables so that PHP can access them. If you're unsure about this, please ask your admin if he could verify that the correct permissions are set.

      > I talked with the Server Admin and he told me that there is a possbility to
      > execute the files outside the safe_mode_exec_dir. The files must be located in
      > the same directory as the script.

      Ok. In that case, you should probably move all of the Bibutils programs to the refbase root directory and try to use a relative path to Bibutils:

      UPDATE depends SET depends_path = "./" WHERE depends_external = "bibutils";

      Alternatively, try to move the Bibutils programs to the refbase 'includes/' directory, and use:

      UPDATE depends SET depends_path = "./includes/" WHERE depends_external = "bibutils";

      Instead of the dot (".") in the above examples, it may be a good idea to try full server paths as well.

      > By the way. There was no chance to setup the database with the install script.
      > I did the first setup with the SQL file in PHPMyAdmin.

      Yes. The refbase 'install.php' script currently does not work on shared hosts. Sorry for the inconvenience.

      > There are several files in the PHPtmp directory, but with the attributes 600
      > this is another problem. I am not able to delete the files and it seems that
      > refdb ist writing the session infos (login) without deleting them.

      refbase does not delete any session files in the PHP temp directory. Session management is handled by PHP itself.

      > But this shows that the Phptmp path is usable.

      Please try to enter the full server path to this PHP temp directory in file 'includes/execute.inc.php', as explained in my last email.

      > But there is another error during uploading files

      > Warning: preg_replace(): Unknown modifier '\'
      > in /home/www/web25/html/uni/refdb/includes/include.inc.php on line 3631

      This is a known issue. You can easily fix this error yourself by following the instructions at:

      http://wiki.refbase.net/index.php/Installation-Troubleshooting#Upload_of_files_results_in_error_message

      HTH, Matthias

       
    • Knut Krüger

      Knut Krüger - 2007-04-03

      Hi Matthias

      > But this shows that the Phptmp path is usable.

      > Please try to enter the full server path to this PHP temp directory in file 'includes/execute.inc.php', as explained in my last
      >email.
      I tried the full path, but there was no success.

      I am out of office since April 16 and I will try to find error.
      In the meantime:

      Do you know a linux test ececutable with php script to test the server config for the script directoy
      Regards Knut

       
      • Matthias Steffens

        > > Please try to enter the full server path to this PHP temp
        > > directory in file 'includes/execute.inc.php', as explained in my
        > > last email.
        > I tried the full path, but there was no success.

        Did you also move the Bibutils programs to the refbase root directory and adjusted the Bibutils path in table 'depends' accordingly?

        Note that you must fulfill *all* of the requirements outlined in my previous emails and on the wiki page to get Bibutils working. In other words, the path to the temp directory might be correctly set now, but Bibutils is still not executable on your server (since it's at a location where PHP is not allowed to access it).

        You could also insert print & exit commands into the refbase PHP scripts (especially in 'execute.inc.php') to debug this issue step by step. However, it may be easiest  to contact your server admin and ask for help with this problem.

        > Do you know a linux test ececutable with php script to test the
        > server config for the script directoy

        I'm not sure what you mean by this. What exactly is it that you want to test? If it's whether Bibutils is recognized at your script directory, then inserting print & exit commands into 'execute.inc.php' may be the best way of doing so.

        It may be also worth to install refbase + Bibutils on a local machine, and get it working there first. Play with it there, by inserting some print & exit commands. When you know how the output is supposed to look like, do the same step-by-step tests on your server.

        Matthias

         
    • Knut Krüger

      Knut Krüger - 2007-04-17

      Hi Matthias,
      I am back ..

      >I'm not sure what you mean by this. What exactly is it that you want to test?
      I would like to test whether it is possible to use executables in that directory
      I talked just with the admin, he tried to execute some executables from the console, no error.  Whatever this means ...

      The requirements:
      Export of records results in a blank page

      At present, the BibTeX, EndNote, and RIS export formats require a correctly configured Bibutils while the MODS XML, ODF XML, and SRW  XML formats do not depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your Bibutils install.

      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:

      mysql> SELECT * FROM depends;

      +------------+------------------+-----------------+--------------+
      | depends_id | depends_external | depends_enabled | depends_path |
      +------------+------------------+-----------------+--------------+
      |          1 | refbase          | true            | NULL         |
      |          2 | bibutils         | true            | NULL         |
      +------------+------------------+-----------------+--------------+
      I tried to set the path:
      absolute: /home/www/web25/html/uni/refdb/
      relative:  ./
      absolute: /home/www/web25/html/uni/refdb/includes
      relative:  ./includes

      no change

      In addition, please note that:

          * the path to the Bibutils programs given in table depends must end with a slash
      yes there is a slash
          * permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP permissions
      Yes the permissions are set like the admin told me 755
          * if safe_mode is set to On in your active php.ini file, then you'll need to put the Bibutils programs within the directory                     *    that's specified in safe_mode_exec_dir

      Safe mode is on but the admin told me it should work in the scriptpath ... hope again he is right

          * the PHP temp/session directory must be accessible & writable by Apache/PHP/Bibutils

      Refdb is able to write the session files - so I think the script is able to use the phptmp directory

          * if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may    *  need to hardcode into file includes/execute.inc.php (line 154, variable $tempDirPath, in function getTempDirPath())

      Yes I changed the path with the absolute path for the php tmp path

      _____________________________________________________________________________________________

      >It may be also worth to install refbase + Bibutils on a local machine, and get it working there first. Play with it there, by >inserting some print & exit commands. When you know how the output is supposed to look like, do the same step-by-step tests on your >server.

      the local machine does have a working refbase but it is a windows machine. Therefore it does not make sense to test linux executables ..

      Sorry for the trouble but installing a unknown software at an internet server is like to be blind and deaf
      but I will try to find any solution

       
    • Knut Krüger

      Knut Krüger - 2007-04-17

      Hi Matthias,

      I changed the safemode to off an it works ... but this is not a solution for the future and I will talk with the admin to find a way to set it on again.
      I will report aou the result

      Regards Knut

       
      • Richard Karnesky

        I really think that you must set 'safe_mode_exec_dir'

        When safe mode is on, this is the only way to execute external programs.  As long as write access is not permitted to the safe_mode_exec_dir & bibutils are the only programs in that directory, this should be secure (unless you consider bibutils insecure, but you don't seem to (as you do want to exec them)).

        If it successfully executes with safe mode off, it implies the executables have their permissions set appropriately & that you give refbase the correct path to them.  The most obvious thing left to check is to make sure you can execute programs in that directory when safe mode is on.

         
    • Knut Krüger

      Knut Krüger - 2007-04-17

      I will get the possibility to set the safe_mode_exec_dir tomorrow.
      Just now it ist set to an no existing path and the field to change the path is missing.
      I think it wil work after setting it to an existing path.

      Regards Knut

       
    • Knut Krüger

      Knut Krüger - 2007-04-18

      Hi mathias
      May I ask again?

      It works with safemode off and the path
      value of the depends path /home/www/web25/files/

      now I was able to set the safe_mode_exec_dir:

      safe_mode_exec_dir    home/www/web25/files

      I tried also with (but I am nearly sure that it is wrong for the PHP Config)
      safe_mode_exec_dir    home/www/web25/files/

      It does not work with the same RefBase configuration and Safemode ON.
      And if safemode is off it is not allowed to set allow_url_fopen to ON
      And setting this feature to OFF will cause an error while importing PubMed records.

      There are no other bibtext executables in the system

       
      • Richard Karnesky

        I don't understand your notation.  Did you enter the line like this:
          safe_mode_exec_dir = "/home/www/web25/files/"
        Can you enable logging of all warnings and errors & check the logfile for something informative?

         
    • Knut Krüger

      Knut Krüger - 2007-04-18

      Aditional info it is PHP Version 4.3.11

       
    • Matthias Steffens

      Is the 'home' directory at your server's root, or somewhere else? I ask since, in the examples you gave earlier, you did specify a full server path in refbase table 'depends', but a relative path (without the leading slash) for 'safe_mode_exec_dir'. If this wasn't just a typo in your post, it's worth trying again with:

      safe_mode_exec_dir /home/www/web25/files

      or

      safe_mode_exec_dir /home/www/web25/files/

      Sorry but I fear that I cannot be of much help with this issue. I don't have any deeper insights about how safe_mode works on different PHP servers (and PHP versions), and I don't have any particular experience with it.

      Matthias

       
    • Knut Krüger

      Knut Krüger - 2007-04-19

      Hi Richard,
      it is a shared server without console access for me
      PHPInfo reports
      safe_mode_exec_dir = /home/www/web25/files
      the files are inside this directory
      file permission 755 directory permissions 755

      I do not get any errors, they appear only in the directories without access for me, anywere at the server.
      Just now it is working but with safe_mode_off and allow_url_open on - a littel bit dangerous. Hope the RefBase script and my Forums software is safe enough.
      but it is not possible to set those settings of my own it was a workaround from the admin. And If I will set anything at the PHP settings by my own this "dangerous" workaround will be gone.

      Regards Knut

       
    • Knut Krüger

      Knut Krüger - 2007-04-23

      Hi Richard,
      I set
      display_errors ON
      display_startup_errors OFF (Default)
      error_reporting 255
      report errors  TRUE
      ignore_repeated_errors    OFF   
      ignore_repeated_source    OFF   
      log_errors ON
      track_errors ON   

      Result: No error - no output

      The admin told me that it is not possible to set the (PHP Version 4.3.11) PHP error loging for each websape.
      The PHP Error lock shows only the complete locking for all useres, but he told me that there was no error, but he found the notice of the other tread.

      Regards Knut

       
    • Knut Krüger

      Knut Krüger - 2007-04-24

      Next I tried to delele the file xml2bib.
      The result was the same as with safemode off.
      but why is there no error message?
      All messages from notice to warnings are set to on, and also notices are appearing at the screen.
      maybe you could see anything at the phpinfo:
      http://uni-regensburg.equine-behaviour.de/phpinf.php

      Regards Knut

       
      • Richard Karnesky

        Could you please write to a logfile?  Relying on displayed errors/warnings is not a good idea, as pages may not be well-formed HTML or you may be redirected, preventing you from seeing an error.  It is better to check the file.

         
    • Knut Krüger

      Knut Krüger - 2007-04-24

      sorry should be
      Next I tried to delele the file xml2bib.
      The result was the same as with *safemode off.*

       
    • Knut Krüger

      Knut Krüger - 2007-04-24

      Hi Richard,
      I would be glad to get a logfile, but the server admin told me that the PHP logfile is only one logfile for the server.
      He told me that it is not possible to split the php logfile depending on shared webserver users.
      Is there any possibilty to write an own logfile?

      But we monitored the logfile:
      I was using RefBase with all errors on.
      He found the notice from this tread:
      http://sourceforge.net/forum/forum.php?thread_id=1720755&forum_id=218758
      Just after reading this notice at the screen and lerading thsi in the logfile i started the export function with save_mode on and no result in the output file.
      There was no error either in the logile or at screen.
      Normally I would think there is any server configuration mismatch, because it seems so that I am the only one with that problem.
      But I need any hint what could be wrong and I feel really blind in this case.

      Regards Knut

       
      • Richard Karnesky

        External logging varies between providers & I'm afraid I can't help you figure out how (or even if) you can set it up.

        How, exactly, did you monitor the logfile?  Many exec problems won't have path information in the log.  Please grep through it for whichever bibutils program(s) you've tried to use.

        I've tried to make our execute functions a bit more robust.  Please try replacing includes/execute.inc.php with
          http://arc.nucapt.northwestern.edu/~karnesky/refbase/execute.inc.php.txt
        (change the extension)

        --Rick

         
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