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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 crcdata 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
Step 1: Change Working Directory
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During the CRC Data Installation 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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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
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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 propertiesAssumptions:
Instructions:1. At the command prompt type the following:
2. The db.properties file will open. Set the following properties for the DBMS at your site:
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<div class="i2b2-panel"> <table class="i2b2-important"> <colgroup> <col width="24"> <col> </colgroup> <tbody> <tr> <td> <img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_important.png" width="16" height="16" align="absmiddle" alt="info" border="0"> </td> <td> <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>. </td> </tr> </tbody> </table> </div> |
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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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<div class="i2b2-panel"> <table class="i2b2-tip"> <colgroup> <col width="24"> <col> </colgroup> <tbody> <tr> <td> <img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_tip.png" width="16" height="16" align="absmiddle" alt="info" border="0"> </td> <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> |
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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. |
Step 3: Create the
crcdataData Repository (CRC) tables, indexes and sequences
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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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<img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_note.png" width="16" height="16" align="absmiddle" alt="info" border="0">
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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
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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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<img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_note.png" width="16" height="16" align="absmiddle" alt="info" border="0">
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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 5: Load sample data into the tables
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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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<div class="i2b2-panel">
<table class="i2b2-note">
<colgroup>
<col width="24">
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</colgroup>
<tbody>
<tr>
<td>
<img src="https://community.i2b2.org/wiki/download/attachments/14091764/icon_note.png" width="16" height="16" align="absmiddle" alt="info" border="0">
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<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.
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Step 6: Create the OMOP views
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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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