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Re: Import to SAS

I tried this briefly but with no luck. My current plans are to use
SAS/Access to ODBC to extract the data from the Postgres datamart directly.
That way I should be able to largely automate the process and apply formats
and labels as I pull the data in.
I'm still awaiting a SAS license at work so haven't started coding yet.
If I need CDISC compatible data I'll re-export it from SAS later using PROC
CDISC.
Rick.
[email protected] writes:
> > I'm sorry to repeat my question, but I haven't got any positive answer ...
> >
> > Could you write me here please, if you are importing the OpenClinica data in CDISC ODM XML format into SAS ?
> > I tried it more ways without success, and I doubt that it is possible without manual corrections of the exported file.
> >
> > Best regards
> > Karel Beber
> >
> >
> >
> >
> >

Comments

  • joshkajoshka Posts: 39
    Hi all,

    Actually in my case, I've failed to export data from OC 2.2. The tab-delimited, SPSS, etc datasets I designed come out as empty (just headers). I'm sure I've entered lots of data in these CRFs.

    Any help will warmly be appreciated.

    Joshua


    On Sat, Apr 26, 2008 at 12:14 AM, Rick Watts wrote:
    I tried this briefly but with no luck. My current plans are to use
    SAS/Access to ODBC to extract the data from the Postgres datamart directly.
    That way I should be able to largely automate the process and apply formats
    and labels as I pull the data in.
    I'm still awaiting a SAS license at work so haven't started coding yet.
    If I need CDISC compatible data I'll re-export it from SAS later using PROC
    CDISC.
    Rick.
    [email protected] writes:
    > I'm sorry to repeat my question, but I haven't got any positive answer ...
    >
    > Could you write me here please, if you are importing the OpenClinica data in CDISC ODM XML format into SAS ?
    > I tried it more ways without success, and I doubt that it is possible without manual corrections of the exported file.
    >
    > Best regards
    > Karel Beber
    >
    >
    >
    >
    >
  • Paul GalvinPaul Galvin Posts: 886
    Hi Joshua,

    Before any data can be extracted from OpenClinica you will need to run the pg_data_warehouse.sql script on the openclinica database you have set up. The script creates a table called extract_data_table and puts all of the information that can be extracted in there.

    The script can be found in the oc/OpenClinica-2.2/config/datawarehouse folder. After running the file, please let us know if you can extract data.
    Thanks,
    Paul
    Sent: Sunday, April 27, 2008 11:25 AM
    To: [email protected]
    Subject: Re: [Users] Re: Import to SAS

    Hi all,

    Actually in my case, I've failed to export data from OC 2.2. The tab-delimited, SPSS, etc datasets I designed come out as empty (just headers). I'm sure I've entered lots of data in these CRFs.

    Any help will warmly be appreciated.

    Joshua


    On Sat, Apr 26, 2008 at 12:14 AM, Rick Watts wrote:
    I tried this briefly but with no luck. My current plans are to use
    SAS/Access to ODBC to extract the data from the Postgres datamart directly.
    That way I should be able to largely automate the process and apply formats
    and labels as I pull the data in.
    I'm still awaiting a SAS license at work so haven't started coding yet.
    If I need CDISC compatible data I'll re-export it from SAS later using PROC
    CDISC.
    Rick.
    [email protected] writes:
    > I'm sorry to repeat my question, but I haven't got any positive answer ...
    >
    > Could you write me here please, if you are importing the OpenClinica data in CDISC ODM XML format into SAS ?
    > I tried it more ways without success, and I doubt that it is possible without manual corrections of the exported file.
    >
    > Best regards
    > Karel Beber
    >
    >
    >
    >
    >
  • joshkajoshka Posts: 39
    Hi Paul,

    I actually ran the pg_data_warehouse batch file in the begining which of course runs the sql script. I've checked the extract_data_table is already created in pgAdminIII. But still the extraction won't work.

    Pls let me know if there are any other configs I need to do.

    Thanks,
    Joshua


    On Mon, Apr 28, 2008 at 1:04 PM, Paul Galvin wrote:
    Hi Joshua,

    Before any data can be extracted from OpenClinica you will need to run the pg_data_warehouse.sql script on the openclinica database you have set up. The script creates a table called extract_data_table and puts all of the information that can be extracted in there.

    The script can be found in the oc/OpenClinica-2.2/config/datawarehouse folder. After running the file, please let us know if you can extract data.
    Thanks,
    Paul
    Sent: Sunday, April 27, 2008 11:25 AM
    To: [email protected]
    Subject: Re: [Users] Re: Import to SAS

    Hi all,

    Actually in my case, I've failed to export data from OC 2.2. The tab-delimited, SPSS, etc datasets I designed come out as empty (just headers). I'm sure I've entered lots of data in these CRFs.

    Any help will warmly be appreciated.

    Joshua


    On Sat, Apr 26, 2008 at 12:14 AM, Rick Watts wrote:
    I tried this briefly but with no luck. My current plans are to use
    SAS/Access to ODBC to extract the data from the Postgres datamart directly.
    That way I should be able to largely automate the process and apply formats
    and labels as I pull the data in.
    I'm still awaiting a SAS license at work so haven't started coding yet.
    If I need CDISC compatible data I'll re-export it from SAS later using PROC
    CDISC.
    Rick.
    [email protected] writes:
    > I'm sorry to repeat my question, but I haven't got any positive answer ...
    >
    > Could you write me here please, if you are importing the OpenClinica data in CDISC ODM XML format into SAS ?
    > I tried it more ways without success, and I doubt that it is possible without manual corrections of the exported file.
    >
    > Best regards
    > Karel Beber
    >
    >
    >
    >
    >
  • Paul GalvinPaul Galvin Posts: 886
    Hi Joshua,
    After you collected data, did you run the pg_data_warehouse script? It is fine to run it when you first created the database, but it is something that needs to be run on a continuous basis to make sure you can extract the latest data collected.

    There are ways to run a scheduled task so the extract_data_table does not have to be created manually and we provide some pointers on what files need to be configured towards the end of the installation document. If you do not set up the scheduled task, you will have to run the pg_data_warehouse manually.

    One final note, if the event CRF does not have a status of Completed, then no data can be extracted. You will need to make sure the CRFs have been Marked Complete during the data entry process.
    Thanks,
    Paul
    Sent: Tuesday, April 29, 2008 8:27 AM
    To: [email protected]
    Subject: Re: [Users] Re: Import to SAS

    Hi Paul,

    I actually ran the pg_data_warehouse batch file in the begining which of course runs the sql script. I've checked the extract_data_table is already created in pgAdminIII. But still the extraction won't work.

    Pls let me know if there are any other configs I need to do.

    Thanks,
    Joshua


    On Mon, Apr 28, 2008 at 1:04 PM, Paul Galvin wrote:
    Hi Joshua,

    Before any data can be extracted from OpenClinica you will need to run the pg_data_warehouse.sql script on the openclinica database you have set up. The script creates a table called extract_data_table and puts all of the information that can be extracted in there.

    The script can be found in the oc/OpenClinica-2.2/config/datawarehouse folder. After running the file, please let us know if you can extract data.
    Thanks,
    Paul
    Sent: Sunday, April 27, 2008 11:25 AM
    To: [email protected]
    Subject: Re: [Users] Re: Import to SAS

    Hi all,

    Actually in my case, I've failed to export data from OC 2.2. The tab-delimited, SPSS, etc datasets I designed come out as empty (just headers). I'm sure I've entered lots of data in these CRFs.

    Any help will warmly be appreciated.

    Joshua


    On Sat, Apr 26, 2008 at 12:14 AM, Rick Watts wrote:
    I tried this briefly but with no luck. My current plans are to use
    SAS/Access to ODBC to extract the data from the Postgres datamart directly.
    That way I should be able to largely automate the process and apply formats
    and labels as I pull the data in.
    I'm still awaiting a SAS license at work so haven't started coding yet.
    If I need CDISC compatible data I'll re-export it from SAS later using PROC
    CDISC.
    Rick.
    [email protected] writes:
    > I'm sorry to repeat my question, but I haven't got any positive answer ...
    >
    > Could you write me here please, if you are importing the OpenClinica data in CDISC ODM XML format into SAS ?
    > I tried it more ways without success, and I doubt that it is possible without manual corrections of the exported file.
    >
    > Best regards
    > Karel Beber
    >
    >
    >
    >
    >
  • joshkajoshka Posts: 39
    Hi Paul,

    Many thanks, it now works fine. What happened that during the time which I had scheduled my .dat to run, my station was powered off. When I ran the .sql file, things worked out fine.

    Just one slight comment about Protected Health Information (PHI) which we specify during CRF creation. I was of the view that info flaged as PHI should not be exported even if users have selected the fields on the exportation screen. I did this for some patients' info including their home contacts and NOK. It skipped my mind not to exclude it during exportation and this was offensive to the PI.

    Kind regards,
    Joshua


    On Tue, Apr 29, 2008 at 2:41 PM, Paul Galvin wrote:
    Hi Joshua,
    After you collected data, did you run the pg_data_warehouse script? It is fine to run it when you first created the database, but it is something that needs to be run on a continuous basis to make sure you can extract the latest data collected.

    There are ways to run a scheduled task so the extract_data_table does not have to be created manually and we provide some pointers on what files need to be configured towards the end of the installation document. If you do not set up the scheduled task, you will have to run the pg_data_warehouse manually.

    One final note, if the event CRF does not have a status of Completed, then no data can be extracted. You will need to make sure the CRFs have been Marked Complete during the data entry process.
    Thanks,
    Paul
    Sent: Tuesday, April 29, 2008 8:27 AM
    To: [email protected]
    Subject: Re: [Users] Re: Import to SAS

    Hi Paul,

    I actually ran the pg_data_warehouse batch file in the begining which of course runs the sql script. I've checked the extract_data_table is already created in pgAdminIII. But still the extraction won't work.

    Pls let me know if there are any other configs I need to do.

    Thanks,
    Joshua


    On Mon, Apr 28, 2008 at 1:04 PM, Paul Galvin wrote:
    Hi Joshua,

    Before any data can be extracted from OpenClinica you will need to run the pg_data_warehouse.sql script on the openclinica database you have set up. The script creates a table called extract_data_table and puts all of the information that can be extracted in there.

    The script can be found in the oc/OpenClinica-2.2/config/datawarehouse folder. After running the file, please let us know if you can extract data.
    Thanks,
    Paul
    Sent: Sunday, April 27, 2008 11:25 AM
    To: [email protected]
    Subject: Re: [Users] Re: Import to SAS

    Hi all,

    Actually in my case, I've failed to export data from OC 2.2. The tab-delimited, SPSS, etc datasets I designed come out as empty (just headers). I'm sure I've entered lots of data in these CRFs.

    Any help will warmly be appreciated.

    Joshua


    On Sat, Apr 26, 2008 at 12:14 AM, Rick Watts wrote:
    I tried this briefly but with no luck. My current plans are to use
    SAS/Access to ODBC to extract the data from the Postgres datamart directly.
    That way I should be able to largely automate the process and apply formats
    and labels as I pull the data in.
    I'm still awaiting a SAS license at work so haven't started coding yet.
    If I need CDISC compatible data I'll re-export it from SAS later using PROC
    CDISC.
    Rick.
    [email protected] writes:
    > I'm sorry to repeat my question, but I haven't got any positive answer ...
    >
    > Could you write me here please, if you are importing the OpenClinica data in CDISC ODM XML format into SAS ?
    > I tried it more ways without success, and I doubt that it is possible without manual corrections of the exported file.
    >
    > Best regards
    > Karel Beber
    >
    >
    >
    >
    >
This discussion has been closed.