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data extraction

I'm trying to perform a data extract. Although data entry was completed, the dataset came up empty.

I think that I need to create a datamart by running the "pg_data_warehouse.sql" script. But how can I run the script?

Is running the “setup_data_warehouse.bat” file enough? Or any ideas?

Thanks.

Ghim Jonglyul, M.D.
Resident
Department of Clinical Pharmacology and Therapeutics, Asan Medical Center
388-1 Pungnap-2dong, Sonpa-gu, Seoul 138-736, Korea
Tel:82-2-3010-4616
Fax:82-2-3010-4623
Mobile:82-19-639-3635
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Comments

  • xfrxfr Posts: 4
    I note that Ghim is in Korea.
    Can you play OpenClinica well with Korean characters?
    What encoding are you using?
    I have difficulty using Chinese using UTF8 encoding...
    Thanks!
    김종률 wrote:
    > > Ghim Jonglyul, M.D.
    > >
    > > Resident
    > >
    > > Department of Clinical Pharmacology and Therapeutics, Asan Medical Center
    > >
    > > 388-1 Pungnap-2dong, Sonpa-gu, Seoul 138-736, Korea
    > >
    > > Tel:82-2-3010-4616
    > >
    > > Fax:82-2-3010-4623
    > >
    > > Mobile:82-19-639-3635
    > >
  • cpeppercpepper Posts: 24
    Ghim

    When I encountered the same problem, I opened Postgresql's PgAdminIII and ran pg_data_warehouse.sql from there. I also found that only completed entries showed up in the extract.
    Sent: Tuesday, August 28, 2007 6:09 AM
    To: [email protected]
    Subject: [Users] data extraction
    I'm trying to perform a data extract. Although data entry was completed, the dataset came up empty.

    I think that I need to create a datamart by running the "pg_data_warehouse.sql" script. But how can I run the script?

    Is running the “setup_data_warehouse.bat” file enough? Or any ideas?

    Thanks.

    Ghim Jonglyul, M.D.
    Resident
    Department of Clinical Pharmacology and Therapeutics, Asan Medical Center
    388-1 Pungnap-2dong, Sonpa-gu, Seoul 138-736, Korea
    Tel:82-2-3010-4616
    Fax:82-2-3010-4623
    Mobile:82-19-639-3635
  • Dear Dr. Jonglyul,

    It will depend on what operating system your server is running on. Under Linux, as the user 'postgres' you can run the following command in the same directory as the script:

    psql -d openclinica -f pg_data_warehouse.sql

    And the datamart will be created. Under Windows, you can use the program pgAdmin (which is usually installed together with Postgres for Windows) to open and run the file. The .bat file is used to set up regular refreshes of the datamart, and will need to be modified to fit your paths. I quote directly from the Install doc for Windows below:

    Execute the C:\OpenClinica\OpenClinica-2.0.1\conf\setup_data_warehouse.bat batch script. This sets seven scheduled tasks, one for each day of the week. One of these commands looks like this:
    AT 00:00 /every:SUNDAY java -cp C:\OpenClinica\OpenClinica-2.0.1\conf;C:\OpenClinica\OpenClinica-2.0.1\conf\postgresql-8.1-405.jdbc3.jar UpdateWarehouseJDBC C:\OpenClinica\OpenClinica-2.0.1\conf\update_warehouse_jdbc.properties
    You may need to change the paths in setup_data_warehouse.bat to fit your installation folders.
    You can run AT with no parameters to verify that the jobs have been loaded.
    You will probably need to change the parameters in update_warehouse_jdbc.properties with the location of the pg_data_warehouse.sql file, and the database name, user, and password.

    Please write more if you have any other questions about setting up the datamart.

    Sincerely,
    Tom Hickerson
    Akaza Research
  • It should be worth noting that all of our pages will support UTF-8 encoding in the upcoming release, due out in October. We would certainly appreciate any feedback on this, once the alpha release is in place!

    Thanks, Tom
  • Good Day;

    I have set OpenClinica recently on my local machine. I also created atest study with CRF and some subjects with events. I fill some data ""can see it in postgresql tables of openclinca database" . Almost every thing seems to work fine except when I try to extract the data the table always empty eventhough data entry is OK.
    I configured and ran "UpdateWarehouseJDBC" by bat, java and from postgres admin i always have empty table with headers nothing more.

    Subject data is partially completed.

    I can select any data from any table using sql queries except when I use "UpdateWarehouseJDBC" I got empty table

    Any help please

    Thanks

    Nasser
  • Have you tried executing “pg_data_warehouse.sql”? This will set up datamart manually. And make sure all CRFs you are going to extract have been marked complete.

    Thanks,

    Yufang Wang
    Akaza Research
    400 One Kendall Square
    Cambridge, MA 02139
    tel: 617.621.8585 x.26
    www.akazaresearch.com
    www.openclinica.org
    Open Source Platform for Clinical Research
    ~ OpenClinica Enterprise ~ Ask me about professional training, support, and services for OpenClinica
    Sent: Wednesday, October 24, 2007 9:37 AM
    To: [email protected]
    Subject: [Users] data extraction

    Good Day;

    I have set OpenClinica recently on my local machine. I also created atest study with CRF and some subjects with events. I fill some data ""can see it in postgresql tables of openclinca database" . Almost every thing seems to work fine except when I try to extract the data the table always empty eventhough data entry is OK.
    I configured and ran "UpdateWarehouseJDBC" by bat, java and from postgres admin i always have empty table with headers nothing more.

    Subject data is partially completed.

    I can select any data from any table using sql queries except when I use "UpdateWarehouseJDBC" I got empty table

    Any help please

    Thanks

    Nasser
  • mishral2mishral2 Posts: 5
    I am having an issue with data extraction.

    The OpenClinica sytem was running in production with v 1.3. Recently I upgraded it to OpenClinica 2.2.1. All the existing information got updated to 2.2.1. Application looks good (along with the data) except the data extraction part. When I clink on creating the dataset, it returns blank dataset.It looks like I am missing something on this part. If i run the sql script to to create the warehouse it goes on for ever. never stops....Any guidance will be greatly appreciated.


    Thank you,

    Leena Mishra

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  • mishral2mishral2 Posts: 5
    I am having an issue with data extraction.

    The OpenClinica sytem was running in production with v 1.3. Recently I upgraded it to OpenClinica 2.2.1. All the existing information got updated to 2.2.1. Application looks good (along with the data) except the data extraction part. When I clink on creating the dataset, it returns blank dataset.It looks like I am missing something on this part. If i run the sql script to to create the warehouse it goes on for ever. never stops....Any guidance will be greatly appreciated.


    Thank you,

    Leena Mishra

    Discover videos like never before. Search and explore on http://www.live.com/ - video search by MSN. Try it!
  • From: leena mishra [mailto:[email protected]]
    Sent: Friday, July 25, 2008 3:22 PM
    To: [email protected]; [email protected]
    Subject: [Developers] Data extraction
    Dear All,

    I am having an issue with data extraction.

    The OpenClinica sytem was running in production with v 1.3. Recently I upgraded it to OpenClinica 2.2.1. All the existing information got updated to 2.2.1. Application looks good (along with the data) except the data extraction part. When I clink on creating the dataset, it returns blank dataset.It looks like I am missing something on this part. If i run the sql script to to create the warehouse it goes on for ever. never stops....Any guidance will be greatly appreciated.


    Thank you,

    Leena Mishra

    Discover videos like never before. Search and explore on http://www.live.com/ - video search by MSN. Try it!
  • mishral2mishral2 Posts: 5
    Thank you,

    Leena
    Subject: RE: [Developers] Data extraction
    Date: Fri, 25 Jul 2008 15:32:59 -0400
    To: [email protected]; user[email protected]
    CC:
    Leena, hi since we got together yesterday I got back to working on my test of 1.1. We need to get to the database to do something I think. First of all, we should really think about dropping the test data extraction rows from 3 tables and get to what we really need. I am doing this on my test PC. Also, the data is supposed to saved in the Tomcat folders (we checked) and that is the part that is missing. The dataset table is trying to reference a physical location that is no longer there. Let me test out a few things and get back to you.
    From: leena mishra [mailto:[email protected]]
    Sent: Friday, July 25, 2008 3:22 PM
    To: [email protected]; [email protected]
    Subject: [Developers] Data extraction
    Dear All,

    I am having an issue with data extraction.

    The OpenClinica sytem was running in production with v 1.3. Recently I upgraded it to OpenClinica 2.2.1. All the existing information got updated to 2.2.1. Application looks good (along with the data) except the data extraction part. When I clink on creating the dataset, it returns blank dataset.It looks like I am missing something on this part. If i run the sql script to to create the warehouse it goes on for ever. never stops....Any guidance will be greatly appreciated.


    Thank you,

    Leena Mishra

    Discover videos like never before. Search and explore on http://www.live.com/ - video search by MSN. Try it!
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