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Data Table Creation - User process
The Create Data Table for export feature allows User to design a table of variables of interest using the Design table feature. The table design can then be saved as a template that can be loaded and used to request data export.
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| Info |
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Wildfly must be restarted for changes to the HIVE_CELL_PARAMs to take effect. |
| Cell ID | Parameter Name | Example Value | Notes |
| CRC | edu.harvard.i2b2.crc.smtp.host | smtp.partners.org | SMTP host |
| CRC | edu.harvard.i2b2.crc.smtp.port | 25 | SMTP port |
| CRC | edu.harvard.i2b2.crc.smtp.ssl.enabled | FALSE | TRUE will enable SSL |
| CRC | edu.harvard.i2b2.crc.smtp.auth | FALSE | TRUE will enable SMTP authentication |
| CRC | edu.harvard.i2b2.crc.smtp.username | none | SMTP username (required for SMTP authentication) |
| CRC | edu.harvard.i2b2.crc.smtp.password | none | SMTP password (required for SMTP authentication) |
| CRC | edu.harvard.i2b2.crc.smtp.enabled | FALSE | TRUE will enable e-mails |
| CRC | edu.harvard.i2b2.crc.exportcsv.defaultescapecharacter | " | Escape character for export files |
| CRC | edu.harvard.i2b2.crc.exportcsv.maxfetchrows | -1 | Maximum number of rows to export, or -1 for no limit |
| CRC | edu.harvard.i2b2.crc.exportcsv.defaultlineend | \n | Line ending for export files |
| CRC | edu.harvard.i2b2.crc.exportcsv.defaultseperator | \t | Field separator for export files |
| CRC | edu.harvard.i2b2.crc.exportcsv.resultfetchsize | 50000 | Number of records retrieved during each database fetch. |
| CRC | edu.harvard.i2b2.crc.exportcsv.filename | {{{PROJECT_ID}}}/{{{DATE_yyyyMMdd}}}_{{{FULL_NAME}}}.tsv | Parameterized template for export file names. If the extension is .zip, the file is zipped. |
| CRC | edu.harvard.i2b2.crc.exportcsv.defaultquotechar | " | Quote character for export files |
| CRC | edu.harvard.i2b2.crc.exportcsv.workfolder | /tmp/i2b2 | Folder on the i2b2 server for data exports |
| CRC | edu.harvard.i2b2.crc.exportcsv.zipencryptmethod | none | Encryption method for the exported ZIP file. One of STANDARD, NONE, or AES. |
PM_PROJECT_PARAMS
The parameters for the emails sent to the project's Data Manager about a data request and to the requesting user when export is complete are set on a per-project basis.
| Parameter Name | Example Value | Notes |
|---|---|---|
| Data Request Template | This user {{{USER_NAME}}} in project {{{PROJECT_ID}}} requested ... | Template text for the body of the data request message; supports placeholders like {{{USER_NAME}}} and {{{PROJECT_ID}}}. |
| Data Request Email Address | someone@somewhere.org | E-mail address of the Data Manager, where the data request e-mail will be sent. |
| Data Request Letter | "Results of the i2b2 request entitled - '{{{QUERY_NAME}}}', ..." | Template text for the e-mail to the user announcing the successful completion of the data export; supports placeholders like {{{QUERY_NAME}}}. |
| Data Request Subject | i2b2 Data Request | Subject line for the data request e-mail. |
| Info |
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The e-mail address for the data request letter (sent when export is complete) is entered in the Query Options Email box at the time of data request submission |
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Template substitution variables (parameters/placeholders inside VALUE)
| Placeholder | Meaning (inferred) | Example |
|---|---|---|
{{{USER_NAME}}} | Display name / username of the requester | Jon Smith |
{{{PROJECT_ID}}} | i2b2 project ID in which the request was run | ACT |
{{{QUERY_NAME}}} | Name/title of the query the user executed | Hypertension Adults |
{{{QUERY_STARTDATE}}} | Timestamp when the query was submitted | 2025-09-19 09:42 |
{{{QUERY_MASTER_ID}}} | Internal i2b2 Query Master ID of the request | 5412 |
{{{PATIENT_COUNT}}} | Number of patients returned by the request | 1999 |
Design and Architecture
The i2b2 breakdown architecture is modified to support the data table definition and new breakdown types for User created data requests. The database tables have been modified to support the data table definitions.
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- The select statement in the VALUE column is executed for the default table data file creation. The result_instance_id value of the query is inserted dynamically each time of data file is created for the same table_instance_id. and does not store in the QT_BREAKDOWN_PATH
- The select statement in the VALUE column of the <data request name>.CSV for the data request is executed to create the data file.
| Info |
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| Currently,1.8.1 request submission send out one email per request selected to the User. |
Software Changes:
- Data: Entries in RPDO_TABLE_REQUEST, HIVE_CELL_PARAMS, PM_PROJECT_PARAMS, QT_QUERY_RESULT_TYPE, and QT_BREAKDOWN_PATH, QT_XML_RESULT define the data exporter functionality.
- Java code: New breakdown classes and updates to existing java classes to support the data exporter functionality.
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