p21-script

A Python script to import inpatient treatment data according to §21 KHEntgG into the AKTIN DWH

The script is intended to import csv files with inpatient treatment data according to §21 KHEntG into the local i2b2 database of the AKTIN DWH. All data is uploaded into the observation_fact table of i2b2. Following requirements must be met by the csv files:

• all csv files must be uploaded together as a zip archive
• all files must be encoded in UTF-8
• the semicolon ; is used as a separator for data fields
• the comma , is used as a separator for decimals

The processes look like following:

An import is currently only possible of the four files fall.csv, fab.csv, icd.csv and ops.csv. The zip archive must contain at least the file fall.csv. The other csv files are optional. All other files will be ignored by the import script.

Of the columns contained in the individual csv files, only selected ones are imported. The following table shows the importable columns. Columns that are not listed are ignored.

CSV file	Column/§21-Variable	Mandatory variable?
fall.csv	KH-internes-Kennzeichen	yes
fall.csv	IK-der-Krankenkasse
fall.csv	Geburtsjahr
fall.csv	Geschlecht
fall.csv	PLZ
fall.csv	Aufnahmedatum	yes
fall.csv	Aufnahmegrund	yes
fall.csv	Aufnahmeanlass	yes
fall.csv	Fallzusammenführung
fall.csv	Fallzusammenführungsgrund
fall.csv	Verweildauer-intensiv
fall.csv	Entlassungsdatum
fall.csv	Entlassungsgrund
fall.csv	Beatmungsstunden
fall.csv	Behandlungsbeginn-vorstationär
fall.csv	Behandlungstage-vorstationär
fall.csv	Behandlungsende-nachstationär
fall.csv	Behandlungstage-nachstationär
fab.csv	KH-internes-Kennzeichen	yes
fab.csv	Fachabteilung	yes
fab.csv	FAB-Aufnahmedatum	yes
fab.csv	FAB-Entlassungsdatum
fab.csv	Kennung-Intensivbett	yes
icd.csv	KH-internes-Kennzeichen	yes
icd.csv	Diagnoseart	yes
icd.csv	ICD-Version	yes
icd.csv	ICD-Kode	yes
icd.csv	Lokalisation
icd.csv	Diagnosensicherheit
icd.csv	Sekundär-Kode
icd.csv	Sekundär-Lokalisation
icd.csv	Sekundär-Diagnosensicherheit
ops.csv	KH-internes-Kennzeichen	yes
ops.csv	OPS-Version	yes
ops.csv	OPS-Kode	yes
ops.csv	Lokalisation
ops.csv	OPS-Datum	yes

Only valid encounter of a csv file are imported, i.e. the necessary fields of an encounter are complete and correspond to the formatting specifications set by the InEK GmbH. A distinction is made between mandatory and optional fields. An invalid mandatory field leads to the exclusion of the whole encounter. An invalid optional field will be ignored during the import.

As the inpatient treatment data is only an extension of the routine documentation of the emergency departments stored in the AKTIN DWH, all valid encounters from the §21 data must be matched with existing encounters from the routine documentation. Matching with existing encounters is done using the field KH-internes-Kennzeichen of the csv files and the field billing id (or alternatively encounter id) of the imported CDA documents.

Usage

The script is only suitable for usage on the AKTIN DWH V1.4 or higher. For the installation of the script on the AKTIN DWH, following steps are necessary:

• Put the script on the server of your AKTIN DWH into the folder /var/lib/aktin/import-script/
• Change the owner of the script to be wildfly:wildfly
• Restart your AKTIN DWH
• The script should appear in the view of the AKTIN DWH in the tab Daten-Import.
• Select the script and import your data

Local Usage

It is also possible to run the script manually. For this, the path to the zip file to be uploaded must be passed to the script as an input argument:

python p21import.py {path to the zip file}

When executing the script via the AKTIN DWH, some information is transmitted as environment variables. For local execution the following variables must be set accordingly:

Parameter	Description	Example
script_id	ID of p21import.py (see @ID=****)	p21
script_version	Version of p21import.py (see @VERSION=****)	1.5
uuid	UUID of the uploaded zip file on the AKTIN DWH	e296bf5c-46b3-11ec-81d3-0242ac130003
username	User of the i2b2 database	username
password	Password of the database user	password
connection-url	Connection url to the i2b2 database	jdbc:postgresql://localhost:5432/i2b2
path_aktin_properties	Path to the aktin.properties	/etc/aktin/aktin.properties

Testing

For testing the script, the folder test/ is attached. The subfolders perform the following functions :

• integration/ : All tests that require a database connection. Currently Unfinished.
• local/ : Script with dummy configuration to run p21import.py locally
• resources/ : Test data used by all tests
• unit/ : Unit tests for p21import.py