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Import data into an I2B2 DB schema

Project description

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I2B2 Import

Introduction

This library provides functions to import data into an I2B2 DB schema.

Installation

Run: pip install i2b2_import

Usage

To import brain features and other observations from a CSV file, use:

observationfact_csv_import.csv2db(file_path, db_conn, src)
    Import brain features and other observation facts data from a CSV file into the I2B2 DB schema.
    * param file_path: Path to the CSV file.
    * param db_conn: Connection to the I2B2 DB.
    * param src: Data source (e.g. CHUV, ADNI, PPMI, etc).

To import metadata from an XML file following the PPMI practice, use:

ppmi_xml_import.PPMIXMLImport.meta2i2b2(source, db_conn):
    The function that imports meta data from PPMI XML file into the I2B2 schema.
    * param source: XML file containing PPMI meta data.
    * param db_conn: Connection to the I2B2 DB.

To import metadata from the data-catalog-db, use:

datacatalogdb_import.DataCatalogDBImport.meta2i2b2(source, db_conn)
    The function that imports meta data from the MRI DB into the I2B2 schema.
    * param source: Connection to the MRI DB.
    * param db_conn: Connection to the I2B2 DB.

Test

Open the tests directory and run ./test.sh.

NOTE: Docker is needed.

build

Run ./build.sh.

Push on PyPi

Run ./publish.sh.

(This builds the project prior to pushing it).

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