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Section

Overview of CRC Data Installation

The crcdata tables are part of the Data Repository (CRC) Cell. The following outlines the steps that will be taken during the crcdata installation.

Step 1:   Change your working directory

Step 2:

 

   Set the database properties for the crcdata 

Step 3:

 

   Create the Data Repository (CRC) tables, indexes and sequences

Step 4:

 

   Create the stored procedures

Step 5:

 

   Load sample data into the tables

Step 6:

 

   Create the OMOP views

 
Section

Step 1: Change Working Directory 
Anchor
omop_crcdata_step1
omop_crcdata_step1

During

the

the CRC Data Installation

we

 we will be working with the crcdata directory. Within this directory are the files we will be editing to define the database properties, create the crcdata tables and load the sample data provided with the i2b2 on OMOP data package.


To change your working directory to the crcdata directory enter the following command:

 

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CD YOUR_I2B2_DATA_DIR\i2b2_omop_data\{oracle|sqlserver}\CRCdata

 
Section
 

Excerpt
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                    </th>
                    <th>
                        <b>Important</b>
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                    <td>
                    </td>
                    <td>The change directory command shown above is written for Windows. The command itself is the same for both Linux and Windows with the only exceptions being the slashes in the path name and Linux does not include the "drive".
					<br>
					<ul>
						<li><i>Linux Path:</i> use a forward slash.</li>
						<li><i>Windows Path:</i> use a backward slash.</li>
					</ul>
                    </td>
                </tr>
            </tbody>
        </table>
    </div>

 

 

Section


EXAMPLES:

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Windows Command:  CD C:\opt\data\i2b2_omop_data\oracle\CRCdata

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Linux Command:  CD /opt/data/i2b2_omop_data/oracle/CRCdata

 

Step 2:   Set the database properties for the crcdata tables  Anchoromop_crcdata_step2omop_crcdata_step2

 

Excerpt

As stated earlier each i2b2 database schema has a corresponding directory that contains the data files for installing the data. Each of these directories has a file called db.properties and it needs to be updated with your environment variables.

Steps for setting database properties

Assumptions:

  • You are logged into the command line application for your environment. (Linux: Terminal or Shell Windows: Command Prompt).
  • You have already changed your working directory to the one that is appropriate for this installation.

Instructions:

1. At the command prompt type the following:

 

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      open db.properties

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      db.properties

 

2. The db.properties file will open. Set the following properties for the DBMS at your site:

 

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                    <b>Important</b>
                    <br>For the purpose of this document, when you set the database properties make sure you set the user to <b>i2b2demodata</b> and the project to <b>demo</b>.
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Oracle Database

db.type=oracle

db.username=i2b2demodata

db.password=demouser

db.server=LocationOfYourDatabase:1521:xe

db.driver=oracle.jdbc.driver.OracleDriver

db.url=jdbc:oracle:thin:@LocationOfYourDatabase:1521:xe

db.project=omop

PostgreSQL Database

db.type=postgresql

db.username=i2b2demodata

db.password=demouser

db.driver=org.postgresql.Driver

db.url=jdbc:postgresql://LocationOfYourDatabase/i2b2?searchpath=i2b2demodata

db.project=omop

SQL Server Database

db.type=sqlserver

 db.username=i2b2demodata

 db.password=demouser

 db.driver=com.microsoft.sqlserver.jdbc.SQLServerDriver

 db.url=jdbc:sqlserver://LocationOfYourDatabase:1433;database=demo

 db.project=omop

 

3. Save the changes and close the file.

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                <td>
                    <b>Tip</b>
                    <br>To save yourself steps, DO NOT close your Command Prompt window as you will be continuing to use it throughout the remainder of the installation.
                </td>
            </tr>
        </tbody>
    </table>
</div>

 

Step 3:   Create the Data Repository (CRC) tables, indexes and sequences  Anchoromop_crcdata_step3omop_crcdata_step3

The third step in the crcdata installation process is to create the crcdata tables, indexes and sequences by running the following command:

Select the command line that is appropriate for your environment.

 

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ant -f data_build.xml create_crcdata_tables

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%ANT_HOME%\bin\ant.bat -f data_build.xml create_crcdata_tables

 

 

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                    <b>Note</b>
                    <br>If the command %ANT_HOME% does not work it may be because you did not set your environment variables <i>(For more information, see the Requirements Chapter in the i2b2 Installation Guide)</i>. If you do not wish to set this variable then you will need to replace %ANT_HOME% with the full path to your Ant directory.
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Step 4:   Create the Data Repository (CRC) stored procedures  Anchoromop_crcdata_step4omop_crcdata_step4

The fourth step in the crcdata installation process is to create the stored procedures for the tables

Select the command line that is appropriate for your environment.

 

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ant -f data_build.xml create_procedures

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%ANT_HOME%\bin\ant.bat -f data_build.xml create_procedures

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                    <img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_note.png" width="16" height="16" align="absmiddle" alt="info" border="0">
                </td>
                <td>
                    <b>Note</b>
                    <br>If the command %ANT_HOME% does not work it may be because you did not set your environment variables <i>(For more information, see the Requirements Chapter in the i2b2 Installation Guide)</i>. If you do not wish to set this variable then you will need to replace %ANT_HOME% with the full path to your Ant directory.
                </td>
            </tr>
        </tbody>
    </table>
</div>

 

Step 5:   Load sample data into the tables  Anchoromop_crcdata_step5omop_crcdata_step5

The fifth in the Crcdata installation process is to load the data into the tables by running the following command:

Select the command line that is appropriate for your environment.

 

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ant -f data_build.xml db_load_crc_data

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%ANT_HOME%\bin\ant.bat -f data_build.xml db_load_crc_data

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                </td>
                <td>
                    <b>Note</b>
                    <br>The loading of the Crcdata may take an extended period of time (over several hours) due to the amount of sample data provided.
                </td>
            </tr>
        </tbody>
    </table>
</div>

 

Step 6:   Create the OMOP views  Anchoromop_crcdata_step6omop_crcdata_step6

The sixth and final step in the crcdata installation process is to create the OMOP view by running the following command:

Select the command line that is appropriate for your environment.

 

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ant -f data_build.xml create_omop_views

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%ANT_HOME%\bin\ant.bat -f data_build.xml create_omop_views