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Export dataset

Hi all

I am getting the following error when exporting a dataset from OC:

The extract data job failed with the message:
org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

Many thanks
David


David Murray
Trials Programmer
National Perinatal Epidemiology Unit
University of Oxford
Old Road Campus
Headington
Oxford
OX3 7LF

Tel: 01865 289709
Fax: 01865 289701
Web: http://www.npeu.ox.ac.uk
Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
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Comments

  • dvmurraydvmurray Posts: 14
    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
  • huberhuber Posts: 5
    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
  • huberhuber Posts: 5
    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
  • dvmurraydvmurray Posts: 14
    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
  • dvmurraydvmurray Posts: 14
    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
  • Dear David,

    I’d imagine you could replicate the database onto another server, edit the data using SQL, export, then correct your edits in the export (Perl/Powershell)? And do this in a documented, scripted way in case you discover other troublesome fields and strings?

    It does sound like a bit of work if you are midway through your study and plan to take regular exports?

    Yours,

    Michael
    Sent: 27 November 2012 11:45
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]nclinica.org; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small

    The University of Dundee is a registered Scottish Charity, No: SC015096
  • Dear David,

    I’d imagine you could replicate the database onto another server, edit the data using SQL, export, then correct your edits in the export (Perl/Powershell)? And do this in a documented, scripted way in case you discover other troublesome fields and strings?

    It does sound like a bit of work if you are midway through your study and plan to take regular exports?

    Yours,

    Michael
    Sent: 27 November 2012 11:45
    To: [email protected]; u[email protected]
    Subject: Re: [Developers] Export dataset

    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small

    The University of Dundee is a registered Scottish Charity, No: SC015096
  • Dear David,

    I use Powershell to clean up issues with the XML when exporting to CDISC ODM XML - my export goes ok, but I have to fix the XML:
    http://en.wikibooks.org/wiki/OpenClinica_User_Manual/SAS#Issues_with_importing_CDISC_ODM_1.3

    Yours,

    Michael
    Sent: 27 November 2012 12:53
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Dear David,

    I’d imagine you could replicate the database onto another server, edit the data using SQL, export, then correct your edits in the export (Perl/Powershell)? And do this in a documented, scripted way in case you discover other troublesome fields and strings?

    It does sound like a bit of work if you are midway through your study and plan to take regular exports?

    Yours,

    Michael
    Sent: 27 November 2012 11:45
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small

    The University of Dundee is a registered Scottish Charity, No: SC015096
    The University of Dundee is a registered Scottish Charity, No: SC015096
  • Dear David,

    I use Powershell to clean up issues with the XML when exporting to CDISC ODM XML - my export goes ok, but I have to fix the XML:
    http://en.wikibooks.org/wiki/OpenClinica_User_Manual/SAS#Issues_with_importing_CDISC_ODM_1.3

    Yours,

    Michael
    Sent: 27 November 2012 12:53
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Dear David,

    I’d imagine you could replicate the database onto another server, edit the data using SQL, export, then correct your edits in the export (Perl/Powershell)? And do this in a documented, scripted way in case you discover other troublesome fields and strings?

    It does sound like a bit of work if you are midway through your study and plan to take regular exports?

    Yours,

    Michael
    Sent: 27 November 2012 11:45
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small

    The University of Dundee is a registered Scottish Charity, No: SC015096
    The University of Dundee is a registered Scottish Charity, No: SC015096
  • huberhuber Posts: 5
    Hi David,

    In response to your query below, I also tried a handful of export formats, but couldn’t get beyond the error until I uploaded new versions of the unrelated worksheets with HTML tags removed. Hopefully Michael’s workaround will prove productive if it’s more onerous for you to upload a new version.

    Best – Wendy
    Sent: Tuesday, November 27, 2012 6:13 AM
    To: [email protected]; [email protected]
    Subject: Re: [Users] Export dataset

    Dear David,

    I use Powershell to clean up issues with the XML when exporting to CDISC ODM XML - my export goes ok, but I have to fix the XML:
    http://en.wikibooks.org/wiki/OpenClinica_User_Manual/SAS#Issues_with_importing_CDISC_ODM_1.3

    Yours,

    Michael
    Sent: 27 November 2012 12:53
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Dear David,

    I’d imagine you could replicate the database onto another server, edit the data using SQL, export, then correct your edits in the export (Perl/Powershell)? And do this in a documented, scripted way in case you discover other troublesome fields and strings?

    It does sound like a bit of work if you are midway through your study and plan to take regular exports?

    Yours,

    Michael
    Sent: 27 November 2012 11:45
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi Wendy

    Thank you for your advice. Did you succeed in exporting any data without having to upload a new version of the CRF? I have tried to export a dataset into a variety of formats without any joy. If all else fails I will upload an amended version of the CRF which does not include HTML tags in the Question_number field.

    Many thanks
    David

    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small
    Sent: 26 November 2012 18:34
    To: [email protected]; [email protected]
    Subject: Re: [Developers] Export dataset

    Hi David,

    I had trouble exporting data for the same reason. I knew I had used HTML tags to bold question numbers in two worksheets defining data unrelated to the data I was trying to export. After removing the HTML tags from Question_Number in those unrelated worksheets (and reloading new versions), I was able to export successfully. My take-away was to avoid using HTML tags in this field altogether moving forward.

    Hope this helps,

    Wendy
    Sent: Monday, November 26, 2012 9:32 AM
    To: [email protected]; [email protected]
    Subject: [Users] Export dataset

    Hi all

    I am getting the following error when exporting a dataset from OC:

    The extract data job failed with the message:
    org.xml.sax.SAXParseException: The value of attribute "OpenClinica:QuestionNumber" must not contain the '<' character.

    After some investigation it appears a HTML bold tag used in the question number field of the CRF is the cause of the problem. Has anyone come across this issue and if so how did they successfully export a dataset?

    Many thanks
    David


    David Murray
    Trials Programmer
    National Perinatal Epidemiology Unit
    University of Oxford
    Old Road Campus
    Headington
    Oxford
    OX3 7LF

    Tel: 01865 289709
    Fax: 01865 289701
    Web: http://www.npeu.ox.ac.uk
    Follow us on Twitter Twitter-for-iPhone-App-Icon-Small

    The University of Dundee is a registered Scottish Charity, No: SC015096
    The University of Dundee is a registered Scottish Charity, No: SC015096
This discussion has been closed.