connector_creation_from_scratch
File Import Settings (Extract)
The first step is selecting the file to import and specifying how it should be read. The file is uploaded to the client and stored server-side, associated with the cohort.
Different settings are displayed based on which filetype is selected from Excel, CSV, JSON.
For more information please read the relevant connector documentation:
Furthermore, an extraction tool can be used. This can be used also for e.g. import from a database or other, more complex data inputs.
Specify Headers
After the file is read, the detected columns are listed. This step allows reviewing and adjusting column names before mapping:
- Rename a column to a more meaningful name. Renamed names carry forward into the mapper and into future re-uploads.
- When Has header row is disabled, columns are assigned numeric names (
0,1,2, ...) which can be renamed here.
Transformation (Transform)
Optionally, transformation tools can be selected. Examples for this is e.g. a conversion from pounds to kg.
Mapper
The mapper step assigns each source column to a field in the data standard. The mapper presents a table with all columns and a sample value from the first row of the file.
For each column, the corresponding field in the schema tree is selected using the Map to Field option. When mapping, we show a preview of the normalization and validation later done on one sample value. You can find more information on the validation in the guidelines and extensive validation rules documentation.
Timeseries mapping
When a column contains multiple measurements per patient recorded over time (e.g. serial lab results), it should be mapped as a timeseries.
A timeseries mapping tells the importer that values in that column are time-anchored, so each measurement is stored individually with its point in time rather than overwriting a single value per patient.
To configure a timeseries mapping, use the Map to Visit/Time option for the relevant column. A dialog will ask for:
| Field | Description |
|---|---|
| Visit | The column that identifies a visit or session. Measurements sharing the same visit ID are grouped together. Useful when multiple readings belong to the same clinical encounter. |
| Time | The column in the file that contains the date or datetime of each measurement. Used to order records chronologically and align series across patients. |
| Timestamp format | The format of the timestamp values, e.g. yyyy-MM-dd HH:mm:ss or epoch. A list of common formats is provided. |
Columns designated as timestamp or visit ID carriers are automatically marked as Timeseries Column in the mapper and cannot themselves be mapped to schema fields, since their role is to provide temporal context rather than clinical values.
Save / Save and Run (Load)
Once the mapping is complete, the connector can be saved or saved and run immediately.
- Save - Stores the connector configuration without importing data. The connector can be run manually at any time from the connector overview.
- Save and Run - Saves the configuration and display the screen from where the import operation can be initialized for loading data into the cohort.