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Steps 1
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Set up a project as documented here:
- Project Setup: Create a project. In this step, you define a project path which will be used to reference the project later.
- When adding users to the project:
- Add the user AGG_SERVICE_ACCOUNT and assign it the role DATA_AGG.
- Add any regular users and assign them the role DATA_OBFSC
- When adding users to the project:
Step 2:
Update DB_Lookup tables to define the Wildfly XML datasource name for the project. Refer to 6.4.3 Cell DB-Lookup: for details.
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Ontology and Workplace cells can also be set up using Project Setup. |
Add new db_lookup entries for each of the core cells, to define how the project will connect to the db.
- The core cells are Ontology, CRC, and Workplace.
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- In i2b2 1.7.13 and
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- above, this step is more easily done directly in the database. Add entries to xxx_db_lookup, for each of ONT, CRC, and WORK.
- Add entries as below, with the project path you defined. It is easiest to copy these from an existing project.
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For ONT_DB_LOOKUP and workplace_db_look up, c_project path does not have a beginning backslash |
Step 3:
Update DATASOURCE XML files IN WILDFLY IF NEEDED …The CRC cell . The data source is defined in the ds-xml file with parameters to connect to the hive and data tables.
i2b2 Server communicates with your i2b2db instance via the configurations set in crc-using ds.xml files. For detailed information refer to 2. Data Source Configuration, or, for an example of setting up data sources for OMOP: Configure Data Sources The datasource parameter should be set in the CRCBootStrapDS section to point to the datasource of the CRC_DB_LOOKUP table. The datasource
The datasource parameter value can be found in the CRC_DB_LOOKUP.C_DB_DATASOURCE (this is built at the time of datamart creation)
The datasource parameter should be set in the QueryToolDemoDS section to point to the datasource of your Crcdata tables location (star-schema and QT tables)
Example: SQL Server crc-ds.xml
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The pool-name parameter and the jndi-name value for the Bootstrap connection section should be set to constant value as CRCBootStrapDS The pool-name parameter and the jndi-name value for the db connection section should be set to the parameter DB_Lookup.C_DB_Data source value |
Step 4:
Load i2b2 tables into the database(s) used for the project as needed, making sure to update db properties file with the db parameters (e.g., 3.4 Crcdata Tables, 3.7.4 Load Metadata Tables). For example, you might specify an existing database in the ontology db-lookup, but a new database in the CRC db lookup. In this case, you only need to create/load the tables in the CRC database.
Step
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5:
Finally add project users. Make sure to add AGG_SERVICE_ACCOUNT
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