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Using the Bulk Data Import

Hello,
Are there some instructions on using the
"Bulk Data Import" described at:
http://www.openclinica.org/dokuwiki/doku.php?id=ocfeatures:openclinica2.5#bulk_data_import
My goal is to play around with this because we have
data in a homegrown system that exports CDISC ODM 1.3
and I would love to get into OpenClinica.
I have the sample database "Docetaxel in Patients With
Completely Resected NSCLC" loaded and I tried
datasets/1/2008/09/23/155016665/Initial_Treatment_-_Phys_Exam_-_BasicD20080923155016-0400.xml
It reports this error:
Alerts & Messages
Passed XML Validation...
Passed Study Check...
Passed OID Metadata Check...
Passed Event CRF Status Check...
Your Item Group OID IG_PHYS_UNGROUPED-F_PHYS_ENGL for Form OID F_PHYS_ENGL does not reference a proper Item Group in that CRF Version.
By the way, where is the XML Validation code?
Thank you,
--
Joshua Daniel Franklin
Biomedical Informatics Core
Institute of Translational Health Sciences
Phone: 206-616-7356 Mail: Box 357420
University of Washington, Seattle 98195

Comments

  • Hi Joshua,
    On the page you referenced is a document you can download with
    instructions on how to create the import file. We will be updating that
    document with some more information, but it should still be helpful.
    The reason the import did not work is the Item Group OIDs contain '-'.
    In 2.5.x, these dashes are not allowed in the OIDs. The reason you see
    the dash in the ODM extract is for legacy data for OpenClinica prior to
    2.2 where repeating groups were not allowed. I've attached an email
    that I wrote a while back before you joined the user's list with the
    explanation of why the '-' appears.
    If you remove the the '-' and everything after that from the
    ItemGroup_OID (for example-F_PHYS_ENGL), you will be able to import the
    data.
    Please let us know if that helps.
    Thanks,
    Paul
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Joshua Daniel
    Franklin (UW Seattle)
    Sent: Monday, November 24, 2008 7:05 PM
    To: [email protected]
    Subject: [Users] Using the Bulk Data Import
    Hello,
    Are there some instructions on using the
    "Bulk Data Import" described at:
    http://www.openclinica.org/dokuwiki/doku.php?id=ocfeatures:openclinica2.
    5#bulk_data_import
    My goal is to play around with this because we have
    data in a homegrown system that exports CDISC ODM 1.3
    and I would love to get into OpenClinica.
    I have the sample database "Docetaxel in Patients With
    Completely Resected NSCLC" loaded and I tried
    datasets/1/2008/09/23/155016665/Initial_Treatment_-_Phys_Exam_-_BasicD20
    080923155016-0400.xml
    It reports this error:
    Alerts & Messages
    Passed XML Validation...
    Passed Study Check...
    Passed OID Metadata Check...
    Passed Event CRF Status Check...
    Your Item Group OID IG_PHYS_UNGROUPED-F_PHYS_ENGL for Form OID
    F_PHYS_ENGL does not reference a proper Item Group in that CRF Version.
    By the way, where is the XML Validation code?
    Thank you,
    -- Joshua Daniel Franklin Biomedical Informatics Core Institute of Translational Health Sciences Phone: 206-616-7356 Mail: Box 357420 University of Washington, Seattle 98195
  • Paul GalvinPaul Galvin Posts: 886
    Hi Jeroen,

    OpenClinica 3.0 has a web service that allows you to register your subjects in a study systematically instead of manually. Please see the following link for more information.

    https://www.openclinica.org/dokuwiki/doku.php?id=developerwiki:soap-studysubject

    Thanks,
    Paul

    -----------------------------------------------------------------------
    Paul J. Galvin
    Project Manager
    Akaza Research
    781-547-8425
    www.openclinica.org
    ~ OpenClinica Enterprise ~ Ask me about professional training, support, and services for OpenClinica
    ***To search the archives of the User and Developer Forums, please go to http://www.openclinica.org/page.php?pid=107***
    From: Belien, J.A.M. [mailto:[email protected]]
    Sent: Friday, April 09, 2010 8:58 AM
    To: Paul Galvin; [email protected]
    Cc: Parlayan, C.
    Subject: [Users] Using the Bulk Data Import

    Dear Paul,

    We would like to upload a well defined study with over 20000 subjects. From the “Data Import Documentation: How to generate and upload XML properly” I read that as a first step I need to “Collect all the OIDs (Object Identifiers) that the OpenClinica system uses to identify various entities. We will need OIDs for Study, Study Subject, Event Definition, Form, Item Group, and Item.”. I can understand most of the items to be defined up front before importing data. But you can imagine that entering over 20000 subjects before I can do the bulk import is not a job I am looking forward to. Is there a solution to automatically insert those subjects first via bulk import as well or should I generate a “bulk insert sql” via a PostgreSQL script? Or is there another method available?

    Best regards, Jeroen Beliën
    Senior scientist/IT
    Department of Pathology
    Room: ZH 0 E 50
    VU University Medical Center
    Amsterdam
    phone: +31 20 4444025
This discussion has been closed.