We hope you'll join us for our 4/23 webinar on using data tables to apply reference ranges and AE codes in OC4. For more information and to register, visit https://register.gotowebinar.com/register/2882170018956684555

Export dataset

2»

Comments

  • 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
  • dvmurraydvmurray Posts: 21
    Thanks for advice Michael.
    I've found a less technical approach to resolving the issue. Firstly I uploaded a new version of the CRF with the HTML tags removed from the Question_number field and entered new data. I then created a new dataset which I was able to successfully export into the required format. However because the dataset included data from both versions of the CRF the field items were duplicated but with some manual processing these were mapped and renamed.
    It's possible when uploading the amended version the Question_number details of the original version are overwritten, though I maybe wrong.
    Many thanks
    David
    On 27 Nov 2012, at 13:25, "Michael Bluett" wrote:
    > 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
    >
    >
    >
    >
    > 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
    >
    >
    >
    >
    > The University of Dundee is a registered Scottish Charity, No: SC015096
    >
    > The University of Dundee is a registered Scottish Charity, No: SC015096
    >
  • dvmurraydvmurray Posts: 21
    Hi Wendy
    I took your approach and uploaded a new version without the HTML tags, created and exported a dataset which included the data entered using the original version.
    Thank you for all your help!
    David
    On 27 Nov 2012, at 21:04, "Wendy Huber" wrote:
    > 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
    >
    >
    >
    >
    > 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
    >
    >
    >
    >
    > 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.