Changes between Version 3 and Version 4 of i2b2 HowTo Create a Project

Timestamp:

07/16/13 10:08:04 (11 years ago)

Author:

Richard Bramley

Comment:

--

i2b2 HowTo Create a Project

@@ -60 +60 @@
   * db.project.data.username
   * db.project.data.password
-  * db.project.meta.databasename
+  * db.project.meta.databasename [1]
   * db.project.meta.username
   * db.project.meta.password
@@ -86 +86 @@
   * JAVA_HOME
 
-iiii. Edit the following SQL scripts in the following ways:
+iv. Edit the following SQL scripts in the following ways:
 
   * sql/sqlserver/meta/tables/create_sqlserver_metadata_tables.sql
    * Remove the creation of BIRN table.
-   * Rename the ONYX table to something appropriate to the new project's ontology. [1]
+   * Rename the ONYX table to something appropriate to the new project's ontology. [2]
 
   * sql/sqlserver/meta/inserts/schemes_insert_data.sql
-   * Edit the values for C_KEY, C_NAME and C_DESCRIPTION [2]
+   * Edit the values for C_KEY, C_NAME and C_DESCRIPTION [3]
 
   * sql/sqlserver/meta/inserts/table_access_insert_data.sql
-   * Use the ontology table name (from [1]) for C_TABLE_CD and C_TABLE_NAME.
-   * Give the ontology a root node name and use it for C_HLEVEL and C_DIMCODE. [3]
-   * Use the ontology description (from [2] C_DESCRIPTION) for the C_FULLNAME and C_TOOLTIP.
+   * Use the {ontology table name from [2]} for C_TABLE_CD and C_TABLE_NAME.
+   * Give the ontology a root node name and use it for C_HLEVEL and C_DIMCODE. [4]
+   * Use the {ontology description from [3] C_DESCRIPTION} for the C_FULLNAME and C_TOOLTIP.
 
   * sql/sqlserver/work/inserts/workplace_access_insert_data.sql
    * Change the C_TABLE_CD for both records to the project name.
+
+=== 3. Run the project creation scripts
+
+Whilst in the procedures directory do the following commands:
+
+  * sudo su root (And enter your password)
+  * export I2B2_PROCEDURES_HOME=$PWD
+  * bin/project-install/1-project-install.sh [Project Name]
+  * bin/project-install/2-update-datasources.sh [Project Name]
+
+=== 4. Create the ontology
+
+Creating the ontology is beyond the scope of this page.  But if you want to create the minimum required to stop an error when clicking the top-level node of the ontology, run the following SQL script:
+
+  {{{
+  #!sql
+
+  INSERT INTO {MetaData database name from [1]}.dbo.{Ontology table name from [2]}
+           ([C_HLEVEL]
+           ,[C_FULLNAME]
+           ,[C_NAME]
+           ,[C_SYNONYM_CD]
+           ,[C_VISUALATTRIBUTES]
+           ,[C_TOTALNUM]
+           ,[C_BASECODE]
+           ,[C_METADATAXML]
+           ,[C_FACTTABLECOLUMN]
+           ,[C_TABLENAME]
+           ,[C_COLUMNNAME]
+           ,[C_COLUMNDATATYPE]
+           ,[C_OPERATOR]
+           ,[C_DIMCODE]
+           ,[C_COMMENT]
+           ,[C_TOOLTIP]
+           ,[UPDATE_DATE]
+           ,[DOWNLOAD_DATE]
+           ,[IMPORT_DATE]
+           ,[SOURCESYSTEM_CD]
+           ,[VALUETYPE_CD])
+     VALUES
+           (0
+           ,'{Ontology root node name from [4]}'
+           ,'{Ontology description from [3]}'
+           ,'N'
+           ,'CA'
+           ,NULL
+           ,NULL
+           ,NULL
+           ,'concept_cd'
+           ,'concept_dimension'
+           ,'concept_path'
+           ,'N'
+           ,'LIKE'
+           ,'{Ontology root node name from [4]}'
+           ,NULL
+           ,'{Ontology description from [3]}'
+           ,GETDATE()
+           ,NULL
+           ,NULL
+           ,'{A suitable source perhaps Ontology description from [3]}'
+           ,NULL)
+GO
+
+  }}}