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/or other observations) from a CSV file, use:
features_csv_import.csv2db(file_path, i2b2_conn, dataset, config):
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 i2b2_db_url: URL of the I2B2 DB.
* param dataset: Data set name.
* param config: A few settings. It is a dictionary that accepts the following fields:
- pid_in_vid: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a case, you
to enable this flag. This will try to split PatientID into VisitID and PatientID.
- sid_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole study).
E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a sessionID.
* param regions_name_file: CSV file containing the abbreviated regions name in the first column and the full names
in the second column.
or from a folder:
features_csv_import.folder2db(folder, i2b2_conn, dataset, config):
Import brain features and other observation facts data from a folder containing CSV files into the I2B2 DB schema.
* param folder: Folder path
* param i2b2_db_url: URL of the I2B2 DB.
* param dataset: Data set name.
* param config: A few settings. It is a dictionary that accepts the following fields:
- pid_in_vid: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a case, you
to enable this flag. This will try to split PatientID into VisitID and PatientID.
- sid_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole study).
E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a sessionID.
* param regions_name_file: CSV file containing the abbreviated regions name in the first column and the full names
in the second column.
To import metadata from the data-catalog-db, use:
data_catalog_import.catalog2i2b2(data_catalog_conn, i2b2_conn):
Import meta data from the Data Catalog DB to the I2B2 schema.
* param data_catalog_conn: Connection to the Data Catalog DB.
* param i2b2_db_url: URL of the I2B2 DB.
To import metadata from extra files (XML, JSON, …), use:
ppmi_xml_import.meta2i2b2(file_path, db_conn, dataset):
Import meta-data from a file into the I2B2 schema.
* param file_path: File (XML, JSON, ...) containing meta-data for a given dataset (PPMI, EDSD, ...).
* param i2b2_db_url: Connection to the I2B2 DB.
* param dataset: Dataset ID (each dataset uses its own meta-data files format)
or from a folder:
ppmi_xml_import.folder2db(folder, db_conn, dataset):
Import meta-data from files from a given folder (recursive) and for a given dataset into the I2B2 schema.
* param folder: Folder containing meta-data files for a given dataset.
* param i2b2_db_url: URL of the I2B2 DB.
* param dataset: Dataset ID (each dataset uses its own meta-data files format)
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).
Release files for i2b2-import 1.6.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distribution (wheel)
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| Tags | Python 3 |
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