imhr.data.download¶

Classes

class imhr.data.download.Download(isLibrary=False)[source]¶

Bases: object

Download raw data from apache, Box, or REDCap servers.

Methods

Methods

REDCap(path, token, url, content[, payload])	Download data from an Research Electronic Data Capture (REDCap) server.
SFTP(source, destination, hostname, …)	Connect to a remote server using a Secure File Transfer Protocol (SFTP).
SQL(driver, destination, hostname, username, …)	[summary]

REDCap(path, token, url, content[, payload])	Download data from an Research Electronic Data Capture (REDCap) server.
SFTP(source, destination, hostname, …)	Connect to a remote server using a Secure File Transfer Protocol (SFTP).
SQL(driver, destination, hostname, username, …)	[summary]

classmethod REDCap(path, token, url, content, payload=None, **kwargs)[source]¶

Download data from an Research Electronic Data Capture (REDCap) server.

Parameters:

path : str Path to save data. For example: >>> path = '/Users/mdl-admin/Desktop/r33/redcap' token : str The API token specific to your REDCap project and username. This is usually found on the Applications > API page. For example: >>> token = 'D19859823032SFDMR24395298' url : str The URL of the REDCap project. For example: >>> url = 'https://redcap.prc.utexas.edu/redcap/api/'. content : str {report, file, raw, arm, instrument, returnFormat, metadata, project, surveyLink, user, participantList} Type of export. Examples include exporting a report (report), file (file), or project info (project). payload_ : dict or None, optional Manually submit parameters for exporting or importing data. Can be entered within the function for convenience. **kwargs : str or None, optional Additional properties, relevent for specific content types. Here’s a list of available properties: Property Description report_id : str (report, record) The report ID number provided next to the report name on the report list page. cformat : str {csv, json, xml, odm} Format to return data, either csv, json, xml, or odm. Default is json. ctype : str Shape of data. Default is flat. rawOrLabel: str {raw, label} (report, record) TExport the raw coded values or labels for the options of multiple choice fields. rawOrLabelHeaders: str (report, record) TExport the variable/field names (raw) or the field labels (label). exportCheckboxLabel: str Specifies the format of checkbox field values specifically when exporting the data as labels (i.e., when rawOrLabel=label). returnFormat : str Format to return errors. Default is json.

Returns:

log : pandas.DataFrame or None Pandas dataframe of each download request. content : pandas.DataFrame or None Pandas dataframe of all data downloaded. start, end : str Timestamp (ISO format) and name of most recent (end) and first (start) file created in folder. now : str Current timestamp in ISO format.

classmethod SFTP(source, destination, hostname, username, password, **kwargs)[source]¶

Connect to a remote server using a Secure File Transfer Protocol (SFTP).

Parameters:

source : str The directory path to retrieve paticipant data. destination : str The directory path to save paticipant data. hostname : str SFTP hostname. username : str SFTP username. password : str SFTP password. **kwargs : str or None, optional Additional properties, relevent for specific content types. Here’s a list of available properties: Property Description filetype : :str or None Filetype to download. Default is csv.

Returns:

log : pandas.DataFrame or None Pandas dataframe of each download request. content : pandas.DataFrame or None Pandas dataframe of all files downloaded. start, end : str Timestamp (ISO format) and name of most recent (end) and first (start) file created in folder. now : str Current timestamp in ISO format.

Examples

>>> name='r33'; source='/home/utweb/utw1211/public_html/r33'; d='/Users/mdl/Desktop/r33/'; un='utw1211'; pwd='43#!9amZ?K$'
>>> log, start, end, now = download.SFTP(source=s, destination=d, hostname=hostname, username=un, password=pwd)

classmethod SQL(driver, destination, hostname, username, password, database, table, **kwargs)[source]¶

[summary]

Parameters:

type : str {‘MySQL’,’MSSQL’} The type of SQL server. Either MySQL or MSSQL. hostname : str The host name or IP address of the sql server. username : str The user name used to authenticate with the sql server. password : str The password to authenticate the user with the sql server. database : str The database name to use when connecting with the sql server. table : str The table name to use when connecting with the sql server. **kwargs : str or None, optional Additional properties, relevent for specific content types. Here’s a list of available properties: Property Description port : int (report, record) The report ID number provided next to the report name on the report list page.

Returns:

connection : :obj:`mysql.connector.connect <https://dev.mysql.com/doc/connector-python/en/connector-python-api-mysql-connector-connect.html>`__ MySQL connector instance.