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User logs into the web client and accesses create data table for export tool under the Tools plugin
The DESIGN TABLE panel displays list of predefined variables that will be included by default in the data export file. These predefined variables are (by default) Gender, Age, Race
From the Ontology Terms tab, drag and drop additional variables of interest onto the DESIGN TABLE grid. These variables will be added as a list of variables included in the data export. The predefined variables are locked and cannot be unchecked since they are required for every data table. Other variables can be deleted under Actions column to exclude them from the data file.
Aggregation method for the variable can be applied by clicking on the drop down box in the Aggregation Method column to assign aggregate options to each variable
Aggregate Options
The availability of aggregation options depends on the type of concept it aggregates on.
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Aggregation Options | Explanation |
Existence (Yes/No) | Whether the patient has an observation of this concept. This is the default option. |
Count: Number of Concepts | Total number of concepts |
Count: Number of Dates | Total number of dates for the participant |
Count: Number of Encounters | Total number of encounters for the participant |
Count: Number of Facts | Total number of observations |
Count: Number of Providers | Total number of providers for the participant |
Date: First Date | Date of earliest observation |
Date: Last Date | Date of the most recent observation |
Calc: First Value | Minimum value of all numeric values observations |
Calc: Last Value | Maximum value of all numeric values observations |
Calc: Number of Values | count no Total numbe of all numeric values observations |
Calc: Average Value | Average value of all numeric values observations |
Calc: Minimum Value | lowest Lowest value of all numeric values observations |
Calc: Maximum Value | Highest value of all numeric values observations |
Calc: Median Value | Median value of all numeric values observations |
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Status is updated as the Data File is processed. from Submitted to File in Progress to File Available.
Example Export files (all data are fake)
Two files are generated for each data table exported.
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- RPDO_TABLE_REQUEST table stores the default data table parametersdefinitions
- HIVE_CELL_PARAMS has new parameters for global and email configurations and the data file generation location (defaults to the server's drive)
- QT_RESULT_TYPE table will contain a new entry for each data table definition
- QT_BREAKDOWN_PATH will contain a new entry for each data table definition which has the data export execution details.
- QT_XML_RESULT contains metadata about each data request, such as status and e-mail details.
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Below is the list of Actions available based on the User role. (future implementation)
| User Role | Create Data Table | Data Request | Data Request Manager View Details | Data Export/Generate Data file | Change Request Status | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Obfuscated | Enabled | Enabled | Enabled | Disabled | Disabled | |||||
| Aggregate | Enabled | Enabled | Enabled | Disabled | Disabled | |||||
| Protected | Enabled | Enabled | EnabledDisabled | Disabled | ||||||
| LDS | Enabled | Enabled | Enabled | Disabled | Disabled | |||||
| Manager/No LDS | Enabled | Enabled | Enabled | Disabled | Disabled | |||||
| Manager/LDS | Enabled | Enabled | Enabled | Enabled | Enabled | |||||
| Admin | Enabled | Enabled | Enabled | Enabled | Enabled |
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| RPDO_TABLE_REQUEST PARAMETERS | DATA TABLE Values |
|---|---|
| TABLE_REQUEST_ID | auto generated incremental value, corresponding to each concept in the data table. Unique for each concept example: 1282,1283, 1284 |
| TABLE_INSTANCE_ID | unique for each Data table ( same value for all the concepts underneath) example: 17 |
| TABLE_INSTANCE_NAME | Data table definition name |
| USER_ID | data request user |
| GROUP_ID | project id |
| SET_INDEX | auto incremented for each concept row for the table instance |
| C_FACTTABLECOLUMN | "concept_cd" for the fact table or "patient_num" for the patient_dimension |
| C_TABLENAME | corresponds to table storing concept_cd/patient_num( concept_dimension or patient_dimension ) |
| COLUMN_NAME | The column name of the data table definition |
| C_FULLPATH | corresponds to the concept's c_fullname in the ontology table |
| C_COLUMNNAME | usually "concept_path" for concept_dimension |
| C_COLUMNDATATYPE | corresponds to ontology table column value |
| C_OPERATOR | corresponds to ontology table column value |
| C_DIMCODE | corresponds to ontology table column value |
| AGG_TYPE | corresponds to Aggregate option selection in data table definition |
| CONSTRAIN_BY_DATE_TO | corresponds to date constraint option selection in data table definition |
| CONSTRAIN_BY_DATE_TO | corresponds to date constraint option selection in data table definition |
| CONSTRAIN_BY_DATE_FROM | corresponds to date constraint option selection in data table definition |
| CONSTRAIN_BY_VALUE_OPERATOR | corresponds to set value constraint selection in data table definition |
| CONSTRAIN_BY_VALUE_CONSTRAINT | corresponds to set value constraint selection in data table definition |
| CONSTRAIN_BY_VALUE_UNIT_OF_MEASURE | corresponds to set value constraint selection in data table definition |
| CONSTRAIN_BY_VALUE_TYPE | corresponds to set value constraint selection in data table definition |
| CREATE_DATE | corresponds data table definition creation date |
| SHARED | Y (for project and system shared table definitions); N (User table definition) |
| DELETE_FLAG | Y (if deleted) or N |
| C_VISUALATTRIBUTES | values are LA or LH (based on visibility table definitions in the panel) |
| REQUIRED | Y for default variables ( race, age, sex); N for other variables |
| JASON_DATA | logs the table definition variables details needed for the execution of the stored procedure to create the data file |
| GENERATED_SQL | logs the SQL query that is generated by stored procedure call for each variable |
| DELETE_DATE | date of table definition deletion |
| CREATE_DATE | date of table definition creation |
| USE_AS_COHORT | N by default; not used currently |
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QT_QUERY_RESULT_TYPE
The data table definition is logged as a breakdown type in the QT_QUERY_RESULT_TYPE table when the user saves the data table definition.
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| RESULT_TYPE_ID | NAME | DESCRIPTION | DISPLAYTYPE_ID | VISUAL_ATTRIBUTE_TYPE_ID | USER_ROLE_CD | CLASSNAME |
Auto generated number example : 144 | RPDO_<TABLE_INSTANCE_ID> example: RPDO_17 | User-created <Table_Name>Request | CATNUM | LU (User and system shared tables) LP (Project shared tables) | DATA_LDS | edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientRequest |
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