redcap_bridge package

Submodules

redcap_bridge.cli module

Provide CLI for the main functionalities of the redcap bridge

redcap_bridge.cli.main(command_line=None)

redcap_bridge.project_building module

redcap_bridge.project_building.build_project(project_csv, output_file=None, include_provenance=True)

Build a complete RedCap Instrument CSV from a set of template_parts and a project csv file.

Parameters:

• project_csv (str) – Filepath of the project csv file

• output_file (str, None) – Filepath of the resulting, complete project csv (with inserted template_parts. If None, the content is only returned and not saved. Default: None

• include_provenance (bool) – If True, include hidden fields in the project csv that contain git commits of source files Default: True

Returns:

• (list) list containing the lines of the complete project definition

• including the template content

redcap_bridge.project_building.customize_project(project_built_csv, customization_csv, output_file=None)

Fill in a built project csv with project specific customizations.

This can be used to e.g. change the default values of fields or customize the list of experimenters to be selected

Parameters:

• project_built_csv (str) – The filepath to the csv containing the built project (see also build_project)

• customization_csv (str) – The filepath to the csv containing the project customizations

• output_file (str) – The path to save the combined csv. Default: None

Returns:

pandas dataframe csv representation of the customized project definition

Return type:

dataframe

redcap_bridge.project_building.extract_customization(project_csv, export_custom_csv, *template_parts)

Extract custom parts of a project data dict by subtracting template parts

Parameters:

• project_csv (path) – path to the complete project csv file

• export_custom_csv (path) – path to store the resulting customization csv file

• *template_parts ((list)) – list of template parts included in the project

redcap_bridge.project_control module

redcap_bridge.project_control.setup_project(proj_folder, working_dir=None, include_provenance=True)

Build a project csv from its specifications and setup on the server

Parameters:

• proj_folder ((path)) – folder containing the project specification files project.json, structure.csv and customizations.csv

• working_dir ((path)) – directory in which to store temporarily generated project files

• include_provenance ((bool)) – include hidden provenance information in project csv. Default: True

redcap_bridge.project_validation module

redcap_bridge.project_validation.validate_project_against_template_parts(project, *templates)

Validate a built project csv

Parameters:

• project (str, buffer) – Filepath of the csv file or csv buffer of the built project

• templates (str, list) – List of file paths of the template part csvs.

Returns:

True if the validation was successful

Return type:

bool

redcap_bridge.project_validation.validate_record_against_template(record_csv, template_csv)

Validate a RedCap record against a template instrument

Parameters:

• record_csv (path) – path to the record csv of that instrument

• template_csv (path) – path to the template csv of an instrument

Return type:

True

Raises:

ValueError in case of failing validation –

redcap_bridge.server_interface module

redcap_bridge.server_interface.check_external_modules(server_config_json)

Download records from the redcap server.

Parameters:

server_config_json (str) – Path to the json file containing the redcap url, api token and required external modules

Returns:

bool

Return type:

True if required external modules are present

redcap_bridge.server_interface.configure_project_settings(server_config_json)

Setting project specific settings on server

Parameters:

server_config_json (str) – Path to the json file containing the redcap url, api token and required external modules

redcap_bridge.server_interface.download_datadict(save_to, server_config_json, format='csv')

Parameters:

• save_to (str) – Path where to save the retrieved data dictionary

• server_config_json (str) – Path to the json file containing the redcap url and api token

• format ('csv', 'json', 'df') – Format of the retrieved data dictionary

redcap_bridge.server_interface.download_project_settings(server_config_json, format='json')

Get project specific settings from server

Parameters:

• server_config_json (str) – Path to the json file containing the redcap url, api token and required external modules

• format (str) – Return format to use (json, csv, xml, df)

Returns:

(dict|list|xml|df)

Return type:

The project settings in the corresponding format

redcap_bridge.server_interface.download_records(save_to, server_config_json, format='csv', compressed=False, **kwargs)

Download records from the redcap server.

Parameters:

• save_to (str) – Path where to save the retrieved records csv

• server_config_json (str) – Path to the json file containing the redcap url and api token

• format ('csv', 'json') – Format of the retrieved records

• kwargs (dict) – Additional arguments passed to PyCap export_records

redcap_bridge.server_interface.get_json_csv_header_mapping(server_config_json)

Returns:

Mapping of json to csv headers

Return type:

dict

redcap_bridge.server_interface.get_redcap_project(server_config_json)

Initialize a pycap project based on the provided server configuration :param server_config_json: json file containing the api_url and api_token :return: pycap project

redcap_bridge.server_interface.upload_datadict(csv_file, server_config_json)

Parameters:

• csv_file (str) – Path to the csv file to be used as data dictionary

• server_config_json (str) –

  Path to the json file containing the redcap url and api token

  returns:

  (int)

  rtype:

  The number of uploaded fields

redcap_bridge.server_interface.upload_records(csv_file, server_config_json)

Parameters:

• csv_file (str) – Path to the csv file to be used as records

• server_config_json (str) –

  Path to the json file containing the redcap url and api token

  returns:

  (int)

  rtype:

  Number of uploaded records

redcap_bridge.utils module

redcap_bridge.utils.compress_record(csv_file, compressed_file=None)

redcap_bridge.utils.exportCSVtoXLS(csv_file, compressed_file=None)

redcap_bridge.utils.remove_columns(csv_file, compressed_file=None)