IDRT - Integrated Data Repository Toolkit
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What is CSV?

A comma-separated values (CSV) file stores tabular data (numbers and text) in plain text. Plain text means that the file is interpreted a sequence of characters, so that it is human-readable with a standard text editor. Each line of the file is a data record. Each record consists of one or more fields, separated by commas. The use of the comma as a field separator is the source of the name for this file format.

See http://en.wikipedia.org/wiki/Comma-separated_values

You can use tabulator ('\t'), semicolon (';') or comma (',') as a delimiter.

Example Files

CSV Example Files

Import CSV

To start the CSV Import, right click the project in the Import Browser you want to upload data to and select Import Data -> Import CSV.

A new window opens, where you can set different options.

Name

Description

Truncate i2b2 Project?

If you check this, the project will be truncated before the data is uploaded.

Truncate Previous Queries?

This will truncate the previous queries tables.

Database Indexing

Ignore: Don't touch the indexes;
Stop/Start: Stop the indexes before the upload and start them afterwards;
Drop/Create: Drop the indexes before the upload and create them from scratch afterwards.

Set patient_count after import

This will fill the c_totalnum column.

CSV Folder

Here you can select the folder that contains all CSV files you want to upload.

Use PID Generator

This will use the PID Generator, which has to be configured seperately (see Options).

IDAT Options

Select whether your identifying data is in the same or in an extra file.

ID-File

Select the identifying data file here.

Date Pattern

Here you can select the date pattern that your data uses (e.g. dd-MM-yyyy).

Quote Character

Here you can set the quote character, that you use in your CSV files.

Save Settings?

This will save the settings for the next import. Note: The truncate checks are never saved.

If you hit finish the upload starts. You can observe the progress in the progress bar of the Import Browser.

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