Import data into an I2B2 DB schema
Project description
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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