Overview
The Data Exporter functionality enables an i2b2 user to request patient data for the patients found by a desired query. In the configured workflow, data is requested and generated through new breakdown types that can be selected in the Run Query dialog. Users will see "data request" breakdowns, which send an e-mail to a predefined data manager requesting a type of data. The data manager (Manager user role) processes the request by rerunning the query with a special "data export" breakdown. The patient data is exported as a file and stored in a specified location for retrieval.
The patient data export types, request options, and file specifications are configured in the database using specific request type entries and configuration parameters in the database.
Data Export Workflow
Data Request (User Process)
- User logs into webclient and creates and runs a query.
- In the Run Query dialog box, select one or more Data Request checkboxes
- Emails are automatically sent - one to the requester's e-mail, to inform them the request has been made; and one to the specified manager user to inform them to run the user's export request. The query name (in previous queries) is tagged with the query master id, so it can be identified by the manager.
Data Export (Manager Process)
The manager logs into the webclient and finds the query from their e-mail by locating the query master id, which is now part of the title of the previous query.
The manager user then re-runs the previous query. In the Run Query dialog, the manager selects the requested export option in the Data export breakdown list.
It is very important to put the original query master id (or some other identifier that links the export to the request) into the query name. The export letter will contain the query name, and this is the only way to trace the export back to the original request. (Currently there is no way to tie the export directory to the data requester query_master_id.) If the data manager runs the query as a query-in-query, the query name will automatically be populated with this identifier.
The data export runs in the background and the file is generated in a specified folder
- An e-mail is sent to the manager that can be forwarded to the requesting user, to inform them that their export is available and to provide retrieval info.
Sample Letter generated for Data ManagerResults of the i2b2 request entitled - "Demographics_12_48_52", submitted on Apr 18, 2024 1:47:58 PM, are available. Important notes about your data: Only persons specifically authorized and selected (as listed at the top of this letter) can download these files. If additional user access is needed, please ensure the person is listed on your project IRB protocol and contact the i2b2 team. Specifically: Your guideline for the storage of Protected Health Information can be found at: https://www.site.com/guidelines_for_protecting_and_storing_phi.pdf *To download these files* These results are the data that was requested under the authority of the Institutional Review Board. The query resulting in this identified patient data is included at the end of this letter. A copy of this letter is kept on file and is available to the IRB in the event of an audit. Thank you, The i2b2 Team |
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Example Export files (all data are fake)
Demographics
Diagnosis
Data Export Configuration
Design and Architecture
The i2b2 breakdown architecture has been modified to support new breakdown types for data request and export. HIVE_CELL_PARAMS has new parameters for global configuration, the QT_RESULT_TYPE table has new entries for query export types, and the QT_BREAKDOWN_PATH defines the request and export. These are XML documents containing e-mails to send and SQL to execute. These breakdown types display in the run query dialog. User e-mails are sent to the e-mail address of the currently logged-in use. Data Manager e-mails are sent to an address configured in HIVE_CELL_PARAMS, and the data manager e-mail in an export is also saved as a file in the export location. The export file generation location, also configured in HIVE_CELL_PARAMS, is on the local drive hosting the i2b2 application.
Database changes
Currently QT_BREAKDOWN_PATH .value column has datatype of varchar(2000). In order to support the XML structure needed for the Data Exporter, the value column has been modified to CLOB datatype.
Configuring Database Parameters
Request/Export query types: QT_QUERY_RESULT_TYPE
The data request and data export query types are configured as breakdowns in the QT_QUERY_RESULT_TYPE table. VISUAL_ATTRIBUTE_TYPE_ID should be set to LR for Data request and LX for Data export
USER_ROLE_CD should be set to DATA_LDS for Data Request and USER_ROLE_CD should be MANAGER for Data Export.
| NAME | DESCRIPTION | DISPLAYTYPE_ID | VISUAL_ATTRIBUTE_TYPE_ID | USER_ROLE_CD | CLASSNAME |
| PATIENT_DEMOGRAPHIC_REQUEST | Request Demographics Data | CATNUM | LR | DATA_LDS | edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientRequest |
| PATIENT_DEMOGRAPHIC_CSV | Export Demographics Data | CATNUM | LX | MANAGER | edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientDownload |
We recommend data requests be limited to DATA_LDS users (irrespective of Admin path role - admin, user, manager) and data exports be limited to MANAGER users (irrespective of data path role - data_lds, data_agg,data_obf, data_deid). The user role determines if exports/requests are visible and runnable.
| QT_QUERY_RESULT_TYPE | user role | data request | data export |
|---|---|---|---|
DATA_LDS | DATA_LDS | Success | non-display |
MANAGER | MANAGER | non-display | Success |
MANAGER with DATA_LDS | MANAGER | Success | |
MANAGER with DATA_LDS | DATA_LDS | Success |
Request/Export file definition details: QT_BREAKDOWN_PATH
QT_BREAKDOWN_PATH defines e-mail content (for request and export) and SQL code (for export) in the following XML format. Any parameters defined in an export XML override the default in HIVE_CELL_PARAMS (e.g., field separator character.)
| Name | Value |
|---|---|
| <?xml version="1.0"?> |
| <?xml version="1.0"?> <ValueExporter> <Version>[...version number...]</Version> <CreationDateTime><date value></CreationDateTime> <DataManagerEmailMessage>details sent to data Manager on data request</DataManagerEmailMessage> <File> <Filename>[... filename specification..]</Filename> <Query>[... SQL query to generate the data export content...]</Query> <SeparatorCharacter>[...file format seperator...]</SeparatorCharacter> </File> </ValueExporter> |
Example Requests
| NAME | VALUE |
| PATIENT_MEDICATION_CSV | <?xml version="1.0"?> <ValueExporter> <Version>3.02</Version> <CreationDateTime>08/09/2024 12:00:00</CreationDateTime> <RequesterEmailMessage>Your request on {{{PROJECT_ID}}} requested i2b2 request entitled - "{{{QUERY_NAME}}}", submitted on {{{QUERY_STARTDATE}}}, with the query master of {{{QUERY_ID}}}</RequesterEmailMessage> <DataManagerEmailMessage>This user {{{USER_NAME}}} in project {{{PROJECT_ID}}} requested i2b2 request entitled - "{{{QUERY_NAME}}}", submitted on {{{QUERY_STARTDATE}}}, with the query master of {{{QUERY_ID}}}. </DataManagerEmailMessage> <LetterFilename>/{{{USER_NAME}}}/{{{QUERY_MASTER_ID}}}/Readme.txt</LetterFilename> <Letter> Results of the i2b2 request entitled - "{{{QUERY_NAME}}}", submitted on {{{QUERY_STARTDATE}}}, are available. Important notes about your data: - Total number of patients returned in your data request: {{{PATIENT_COUNT}}} - i2b2 reviewer: Only persons specifically authorized and selected (as listed at the top of this letter) can download these files. If additional user access is needed, please ensure the person is listed on your project IRB protocol and contact the i2b2 team. Specifically: - Remove all PHI from computer, laptop, or mobile device after analysis is completed. - Do NOT share PHI or PII with anyone who is not listed on the IRB protocol. Your guideline for the storage of Protected Health Information can be found at: https://www.site.com/guidelines_for_protecting_and_storing_phi.pdf *To download these files* - You must be logged onto your site These results are the data that was requested under the authority of the Institutional Review Board. The query resulting in this identified patient data is included at the end of this letter. A copy of this letter is kept on file and is available to the IRB in the event of an audit. Thank you, The i2b2 Team </Letter> <File> <Filename>/{{{USER_NAME}}}/{{{QUERY_MASTER_ID}}}/Medication.csv</Filename> <Query>SELECT to_char(a.PATIENT_NUM) as "I2B2_PATIENT_NUMBER" ,a.start_date as "START_DATE" ,a.start_date as "END_DATE" ,b.name_char as "MEDICATION_NAME" ,b.concept_cd as "NDC_CODE" ,a.units_cd as "UNIT" ,a.quantity_num as "DOSE_QUANTITY" ,a.modifier_cd as "MODIFIER" ,m.name_char as "MODIFIER_NAME" ,a.instance_num as "INSTANCE_NUM" ,a.location_cd as "FACILITY" ,case v.inout_cd when 'O' then 'Outpatient' when 'I' then 'Inpatient' else 'Unknown' end as "ENCOUNTER_TYPE" ,p.name_char as "PROVIDER" ,a.encounter_num as "ENCOUNTER_NUMBER" FROM observation_fact a INNER JOIN concept_dimension b on a.concept_cd = b.concept_cd and b.concept_path like '\i2b2\Medications\%' JOIN {{{DX}}} c on a.patient_num = c.patient_num LEFT OUTER JOIN provider_dimension p on a.provider_id = p.provider_id JOIN visit_dimension v on a.encounter_num = v.encounter_num and a.patient_num = v.patient_num LEFT OUTER JOIN modifier_dimension m on a.modifier_cd = m.modifier_cd</Query> <SeparatorCharacter>\t</SeparatorCharacter> </File> </ValueExporter> |
| PATIENT_MEDICATION_REQUEST | <?xml version="1.0"?> <ValueExporter> <Version>3.02</Version> <CreationDateTime>08/09/2024 12:00:00</CreationDateTime> <RequesterEmailMessage>Your request on {{{PROJECT_ID}}} requested i2b2 request entitled - "{{{QUERY_NAME}}}", submitted on {{{QUERY_STARTDATE}}}, with the query master of {{{QUERY_MASTER_ID}}}</RequesterEmailMessage> <DataManagerEmailMessage>This user {{{USER_NAME}}} in project {{{PROJECT_ID}}} requested i2b2 request entitled - "{{{QUERY_NAME}}}", submitted on {{{QUERY_STARTDATE}}}, with the query master of {{{QUERY_MASTER_ID}}}. </DataManagerEmailMessage> </ValueExporter> |
Export file format/location and Email parameters set-up: HIVE_CELL_PARAMS
Export File format, location and email server parameters are configurable in the HIVE_CELL_PARAMS.
The <Filename> parameter in the QT_BREAKDOWN_PATH definition will override the default value specified in the HIVE_CELL_PARAMS.
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.exportcsv.datamanageremail | userid@partners.org | Email address used for sending request/export e-mails |
| 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.smtp.from.fullname | Data Manager | Name that e-mails will be sent from. |
| CRC | edu.harvard.i2b2.crc.smtp.from.email | datamanager@site.org | E-mail address that e-mails will be sent from. |
| CC | edu.harvard.i2b2.crc.smtp.subject | i2b2 Data Request | Subject line for 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. |
Export query definition variables
These variables can be used in HIVE_CELL_PARAMS entries and in query export definitions:
Value | Description |
{{{USER_NAME}}} | Current user running query |
{{{PROJECT_ID}}} | The project name |
{{{RANDOM_xxx}}} | A random integer where xxx is the max integer size |
{{{DATE_xxx}}} | Date/Time format, where xxx can be from the table below. The string yyyy-MM-dd would output dates that look like 2022-07-26 |
{{{QUERY_NAME}}} | Query Name |
{{{QUERY_STARTDATE}}} | Query Start date/time |
{{{QUERY_ENDDATE}}} | Query End date/time |
{{{PATIENT_COUNT}}} | Number of patients. |
{{{FULL_NAME}}} | Fullname of user who ran query |
{{{QUERY_MASTER_ID}}} | The query Master ID |
{{{QUERY_RUNTIME}}} | Time to run the query |
{{{FULL_SCHEMA }}} | Used in SQL export definitions. Inserts the full schema name (e.g., 'i2b2.dbo.'). Needed to be sure i2b2 accesses the correct data tables! |
Table of allowable characters in {{{DATE_xxx}}} strings:
| Value | Description | Value | Description |
| G | era | K | hour-of-am-pm (0-11) |
| u | year | k | clock-hour-of-am-pm (1-24) |
| yyyy | 4-digit year | H | hour-of-day (0-23) |
| D | day-of-year | m | minute-of-hour |
| M/L | month-of-year | s | second-of-minute |
| d | day-of-month | S | fraction-of-second |
| Q/q | quarter-of-year | A | milli-of-day |
| Y | week-based-year | n | nano-of-second |
| w | week-of-week-based-year | N | nano-of-day |
| W | week-of-month | V | time-zone ID |
| E | day-of-week | z | time-zone name |
| e/c | localized day-of-week | O | localized zone-offset |
| F | week-of-month | X | zone-offset 'Z' for zero |
| a | am-pm-of-day | x | zone-offset |
| h | clock-hour-of-am-pm (1-12) | Z | zone-offset |
| p | pad next |
Software Changes:
- Data: New entries in HIVE_CELL_PARAMS, QT_QUERY_RESULT_TYPE, and QT_BREAKDOWN_PATH define the exporter configuration.
- Java code: New breakdown classes and updates to existing java classes to support the data exporter functionality.
