| Table of Contents | ||||||
|---|---|---|---|---|---|---|
|
...
Use Case
You have data in a file on disk that you want to load into your database and use with RDMP for cohort building and/or project extractions.
File Types
In order to successfully create a new catalogue from a file you will need a delimited flat file (*.csv, *.txt) or Excel (*.xls).
| Info |
|---|
Delimited flat files are easier to load than Excel Excel files with multiple tabs, formulas, sprawling layouts etc may not be machine readable. In such cases you may wish to export Excel data as csv first and load that. |
It is key that the file loaded doesn’t already exist as a catalogue in RDMP. If the new catalogue is specific to a project please rename the file in relevance with the topic, before starting this process.
| Note |
|---|
This process is sensitive to failure due to:
RDMP system tries its best to cover the errors which can occur at any point of the loading process. Please refer to section - When something goes wrong… of this page for help.Delimited files (e.g. csv) must be properly formatted (e.g. quoting fields with commas, newlines etc). Where there is a problem RDMP will indicate the line number and nature of the problem. For more information see When something goes wrong… |
...
Steps
Step 1 -
...
Open the Catalogues Collection
Click on "Catalogues ( button )" in RDMP top menu
...
Right click on the folder where the catalogue needs to be created and select "Create new catalogue from file…"
...
Select New->From File…
...
Step 2 - Data Source
Pick the file which contains the catalogue. At this stage the format of the file selected doesn't matter as long as it is a file which is data compatible. (Excel or flat file).
...
Fill in the database details
...
UserID / Password (optional): When connecting the database to test if a catalogue can be created in it, the system will use these credentials. If not informed, RDMP will use windows credential by default.
Server: by default, the SQL server which has been setup when RDMP has been installed. It can be changed at this stage if another server exists.
Database: List of all database on the server. This should be where you store your clinical data, not the RDMP database itself.
| Info |
|---|
If the server has been changed, click on the refresh button to update list of databases |
Step 4 - Pipeline
Select a pipeline
If the file imported is a flat file, select: BULK INSERT: CSV Import File.
If the file is in Excel, select: BULK INSERT: Excel File.
...
an appropriate pipeline for reading your file type.
...
| Info |
|---|
RDMP will automatically display the compatible pipeline |
...
based on the file selected. |
Click on Execute
...
Execute to begin the upload process.
Step 5 - Configure Extractability view
...