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Bibutils Path error

  • JohnG16

    JohnG16 - 2014-02-01

    Trying to follow the instructions on setting the path to bibutils. I am on a shared server so do not have root access, and my host refuses to install it. The way I understand the instructions, I can place the bibutils directory in refbase, then create a symlink. Several attempts at doing so all return a 127 error using ln -s /home2/jwgmgcom/public_html/refbase/bibutils/ ./bibutils/

  • Richard Karnesky

    How are you trying to perform the command? You may not have permission to execute 'ln'.
    In any case, it isn't necessary to make this symlink. The following SQL command should work, though this assumes you have the path correct, that the binaries you uploaded are appropriate for the server, and that you have permission to run executables:

    UPDATE depends SET depends_path = "/home2/jwgmgcom/public_html/refbase/bibutils/" WHERE depends_external = "bibutils";
    UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";
    Last edit: Richard Karnesky 2014-02-01
  • TGM

    TGM - 2015-05-07


    I'm trying to import some references (bibtex) into refbase but I don't find the way...

    I tried this bibtext extract :
    Title = {L’archivage du dossier patient : enjeux et principes de mise en œuvre.},
    Author = {Anap},
    Publisher = {Anap},
    Note = {La Direction générale et tous les professionnels mobilisés.},
    Type = {Contraintes liées à l’outil},
    Abstract = {Les établissements de santé sont pour la plupart dans une phase de première informatisation du dossier patient, ce qui soulève la question de son archivage. En outre, le remplacement du dossier patient papier par un dossier informatisé est progressif : la cohabitation du papier et du numérique est à organiser.
    Or les archives d’un établissement constituent le capital informationnel de l’établissement. Leur gestion fait partie de la gouvernance de l’établissement et est du ressort de la direction, d’autant qu’elle concerne des tiers vis-à-vis desquels l’établissement a des responsabilités.
    Seule une politique d’archivage maîtrisée et répondant aux exigences légales, réglementaires et normatives peut donc permettre de s’engager dans la substitution du support papier par le support électronique.
    Ce guide a pour objet de fournir aux directions d’établissements de santé les éléments synthétiques leur permettant de motiver les acteurs indispensables, structurer et gérer l’archivage des dossiers patient papier et informatiques.
    Il fait partie d’un ensemble de documents, tous autoportants et disponibles sur le site Internet de l’Anap, qui correspondent à un premier niveau de prise en considération de l’archivage des dossiers patients.},
    Keywords = {MOTS CLE},
    Series = {domaine du document - à préciser ultérieurement},
    File = {nom_du_fichier.pdf:d\:\chemin_du_fichier\fichier.pdf:PDF},
    URL = {URL},
    Month = sep,
    Year = {2013}

    It works well on the demo server ( user "user")
    It works well too when I import it into Aigaion2 (custom install php errors correction)

    I'm not able to import this in my local refbase instance.
    It runs under Windows8-64.
    I compiled bibutils under Ubuntu (I've followed this tip :

    bib2xml and xml2bib work well (see files)
    bib2xml.exe --version :
    bib2xml, bibutils suite version 5.6 date 2015-01-26

    bib2xml.exe -i unicode -nb bibanap1.bib >bibanap1.xml
    xml2bib.exe -i unicode bibanap1.xml > bibanap2.bib

    I tried different parameters into the depends table with no results

    I tried these update requests (with / or \, all paths with or with no "/" or "\" at the end. :

    full path

    UPDATE depends SET depends_path = "D:/xampp/htdocs/xampp/external/refbase-0.9.6/Bibutils5.6/" WHERE depends_external = "bibutils";

    UPDATE depends SET depends_path = "D:\xampp\htdocs\xampp\external\refbase-0.9.6\Bibutils5.6\" WHERE depends_external = "bibutils";

    relative path eg. ".\Bibutils5.6"

    UPDATE depends SET depends_path = "./Bibutils5.6/" WHERE depends_external = "bibutils";
    UPDATE depends SET depends_path = "./Bibutils5.6" WHERE depends_external = "bibutils";

    UPDATE depends SET depends_path = ".\Bibutils5.6\" WHERE depends_external = "bibutils";
    UPDATE depends SET depends_path = ".\Bibutils5.6" WHERE depends_external = "bibutils";

    Is there some solutions ?

    Actual situation is :
    | depends_id | depends_external | depends_enabled | depends_path |
    | 1 | refbase | true | NULL |
    | 2 | bibutils | true | D:/xampp/htdocs/xampp/external/refbase-0.9.6/Bibutils5.6/ |
    | 3 | pdftotext | true | NULL |

    It's not working (import AND export)



    P.S. It was difficult to install a full refbase "operational".
    I'm testing refbase-0.9.6

  • TGM

    TGM - 2015-05-07

    Addenda :

    I've an error into my database : the tables are prefixed by rb_
    So, I can import some data but ...

    With the same example showed in my previous email I get this :

    title="L{\textquoteright}archivage du dossier patient : enjeux et principes de mise en {\oe}uvre",
    optkeywords="strtoupper({\textquoteright}M{\textquoteright}).strtolower({\textquoteright}OTS{\textquoteright}) strtoupper({\textquoteright}C{\textquoteright}).strtolower({\textquoteright}LE{\textquoteright})",
    optlocation="Initial refbase user (",
    optnote="La Direction g{\'e}n{\'e}rale et tous les professionnels mobilis{\'e}s.",
    optnote="exported from refbase (http://localhost/xampp/external/refbase-0.9.6/show.php?record=13), last updated on Thu, 07 May 2015 18:36:10 +0200",

    I loose many informations eg.

    Abstract, type,...

    Sorry for the partial bas previous post

  • Richard Karnesky

    Your paths are set correctly.

    First, try a known working version of bibutils:

    But also: please enable error logging and inspect your error logs: your output contains function calls that for some reason aren't being processed & I've not seen any other report of this. It is likely that you either have to enable a module or function in XAMPP or possibly need to fix a character set inconsistency (since it is strtoupper/strtolower that aren't working).

  • TGM

    TGM - 2015-05-08

    Thanks Richard. I'll have a look to the logs.
    I cant use bibutils_3.40. They aren't compatible with windows 8-64 Pro.

    I will do the same tests under Ubuntu 15.04 in a few days.

  • Richard Karnesky

    Thanks again for the note. I'm not sure if any of our devs our using Win8, so we haven't tested that. We should, however test with the lastest version of bibutils. I'll do that and get back to you.

    But I still suspect the problem you're seeing has to do with how php is configured on XAMPP.

    Which version of refbase are you using, by the way?


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