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        "author": "Mirco Nasuti",
        "author_email": "mirco.nasuti@chuv.ch",
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            "License :: OSI Approved :: Apache Software License",
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            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
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            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "|CHUV| |License| |Codacy Badge| |CircleCI|\n\nI2B2 Import\n===========\n\nIntroduction\n------------\n\nThis library provides functions to import data into an I2B2 DB schema.\n\nInstallation\n------------\n\nRun: ``pip install i2b2_import``\n\nUsage\n-----\n\nTo import brain features (and/or other observations) from a CSV file,\nuse:\n\n::\n\n    features_csv_import.csv2db(file_path, i2b2_conn, dataset, config):\n        Import brain features and other observation facts data from a CSV file into the I2B2 DB schema.\n        * param file_path: Path to the CSV file.\n        * param i2b2_db_url: URL of the I2B2 DB.\n        * param dataset: Data set name.\n        * param config: A few settings. It is a dictionary that accepts the following fields:\n            - pid_in_vid: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a case, you\n            to enable this flag. This will try to split PatientID into VisitID and PatientID.\n            - sid_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole study).\n            E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a sessionID.\n        * param regions_name_file: CSV file containing the abbreviated regions name in the first column and the full names\n            in the second column.\n\nor from a folder:\n\n::\n\n    features_csv_import.folder2db(folder, i2b2_conn, dataset, config):\n        Import brain features and other observation facts data from a folder containing CSV files into the I2B2 DB schema.\n        * param folder: Folder path\n        * param i2b2_db_url: URL of the I2B2 DB.\n        * param dataset: Data set name.\n        * param config: A few settings. It is a dictionary that accepts the following fields:\n            - pid_in_vid: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a case, you\n            to enable this flag. This will try to split PatientID into VisitID and PatientID.\n            - sid_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole study).\n            E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a sessionID.\n        * param regions_name_file: CSV file containing the abbreviated regions name in the first column and the full names\n            in the second column.\n\nTo import metadata from the data-catalog-db, use:\n\n::\n\n    data_catalog_import.catalog2i2b2(data_catalog_conn, i2b2_conn):\n        Import meta data from the Data Catalog DB to the I2B2 schema.\n        * param data_catalog_conn: Connection to the Data Catalog DB.\n        * param i2b2_db_url: URL of the I2B2 DB.\n\nTo import metadata from extra files (XML, JSON, ...), use:\n\n::\n\n    ppmi_xml_import.meta2i2b2(file_path, db_conn, dataset):\n        Import meta-data from a file into the I2B2 schema.\n        * param file_path: File (XML, JSON, ...) containing meta-data for a given dataset (PPMI, EDSD, ...).\n        * param i2b2_db_url: Connection to the I2B2 DB.\n        * param dataset: Dataset ID (each dataset uses its own meta-data files format)\n\nor from a folder:\n\n::\n\n    ppmi_xml_import.folder2db(folder, db_conn, dataset):\n        Import meta-data from files from a given folder (recursive) and for a given dataset into the I2B2 schema.\n        * param folder: Folder containing meta-data files for a given dataset.\n        * param i2b2_db_url: URL of the I2B2 DB.\n        * param dataset: Dataset ID (each dataset uses its own meta-data files format)\n\nTest\n----\n\nOpen the tests directory and run ``./test.sh``.\n\nNOTE: Docker is needed.\n\nbuild\n-----\n\nRun ``./build.sh``.\n\nPush on PyPi\n------------\n\nRun ``./publish.sh``.\n\n(This builds the project prior to pushing it).\n\n.. |CHUV| image:: https://img.shields.io/badge/CHUV-LREN-AF4C64.svg\n   :target: https://www.unil.ch/lren/en/home.html\n.. |License| image:: https://img.shields.io/badge/license-Apache--2.0-blue.svg\n   :target: https://github.com/LREN-CHUV/i2b2-import/blob/master/LICENSE\n.. |Codacy Badge| image:: https://api.codacy.com/project/badge/Grade/f9c92a26fc2142579d3d2109e16bc606\n   :target: https://www.codacy.com/app/hbp-mip/i2b2-import?utm_source=github.com&utm_medium=referral&utm_content=LREN-CHUV/i2b2-import&utm_campaign=Badge_Grade\n.. |CircleCI| image:: https://circleci.com/gh/LREN-CHUV/i2b2-import.svg?style=svg\n   :target: https://circleci.com/gh/LREN-CHUV/i2b2-import\n\n\n",
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