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PyCap: Python interface to REDCap

Project description

This project is community maintained. Please continue to submit bugs and feature requests, though it’s the community’s responsibility to address them.

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Intro

PyCap is a python module exposing the REDCap API through some helpful abstractions. Information about the REDCap project can be found at http://project-redcap.org/.

Available under the MIT license.

Documentation

Canonical documentation can be found on ReadTheDocs.

Features

Currently, these API calls are available:

  • Export Records
  • Export Metadata
  • Import Metadata
  • Delete Records
  • Import Records
  • Export File
  • Import File
  • Delete File
  • Export Users
  • Export Form Event Mappings
  • Export Reports

Events and Arms are automatically exported for longitudinal projects (see below).

Requirements

  • requests (>= 1.0.0)

    $ pip install requests

Usage

>>> import redcap
# Init the project with the api url and your specific api key
>>> project = redcap.Project(api_url, api_key)

# Export all data
>>> all_data = project.export_records()

# import data
>>> data = [{'subjid': i, 'age':a} for i, a in zip(range(1,6), range(7, 13))]
>>> num_processed = project.import_records(data)

# For longitudinal projects, project already contains events, arm numbers
# and arm names
>>> print project.events
...
>>> print project.arm_nums
...
>>> print project.arm_names
...

# Import files
>>> fname = 'your_file_to_upload.txt'
>>> with open(fname, 'r') as fobj:
...     project.import_file('1', 'file_field', fname, fobj)

# Export files
>>> file_contents, headers = project.export_file('1', 'file_field')
>>> with open('other_file.txt', 'w') as f:
...     f.write(file_contents)

# Delete files
>>> try:
...     project.delete_file('1', 'file_field')
... except redcap.RedcapError:
...     # This throws if an error occured on the server
... except ValueError:
...     # This throws if you made a bad request, e.g. tried to delete a field
...     # that isn't a file

# Delete record
>>> response = project.delete_record('1')

# Export form event mappings
>>> fem = project.export_fem()
...

# Export Reports
>>> reports = project.export_reports(['1','2'])

Installation

Install with pip

$ pip install PyCap

Install extra requirements, which allows returning project data as a pandas.DataFrame

$ pip install PyCap[pandas]

Install from GitHub

$ git clone git://github.com/redcap-tools/PyCap.git PyCap
$ cd PyCap
$ python setup.py install

Contributing

1. Create a virtual environment and activate it

$ python -m venv .venv
$ source .venv/Scripts/activate

2. Install pip-tools.

$ pip install pip-tools

3. Install all project dependencies

$ pip-sync requirements.txt dev-requirements.txt

4. Install the package, with a link to the source code. This ensures any changes you make are immendiate available to test.

$ python setup.py develop

5. Add your changes and make sure your changes pass all tests

$ pytest

Finally, start a pull request!

Citing

If you use PyCap in your research, please consider citing the software:

Burns, S. S., Browne, A., Davis, G. N., Rimrodt, S. L., & Cutting, L. E. PyCap (Version 1.0) [Computer Software]. Nashville, TN: Vanderbilt University and Philadelphia, PA: Childrens Hospital of Philadelphia. Available from https://github.com/redcap-tools/PyCap. doi:10.5281/zenodo.9917

HISTORY

1.1.3 (2020-11-05)

  • API Support
    • Add support for import_metadata endpoint (#145 @JuliaSprenger)
  • Documentation
    • Update contributing.rst with new installation instructions (#135 @njvack)

1.1.2 (2020-11-05)

  • API Support
    • Add support for exportFieldNames call (#125 @chgreer)
    • Add dateRangeBegin and dateRangeEnd parameters to Project.export_records (#124 @chgreer)
  • Package Improvements
    • Use pytest for full test suite (#132)
    • Enforce black and pylint style and formatting on project (#132)
    • Deprecate support for Python 2 (#132)
    • Add pandas as an extra_requires (#132)
  • Documentation
    • Update README with new community support model and how to contribute (#132)

1.1.1 (2020-08-18)

  • Bug Fixes
    • Fix package version parsing for UNIX (#122 @fissell)

1.1.0 (2020-07-16)

  • API Support
    • Add rec_type support in import_records() (#40 @dckc)
    • Add export_checkbox_labels keyword arg to export_records() (#48 Tyler Rivera)
    • Properly backfill requested fields for >6.X servers (#55)
    • Add Export Survey Participant List method (#71)
    • Add filter_logic to export_records (#85 @erikh360)
    • Add forceAutoNumber parameter to import_records() (#86 @CarlosBorroto)
    • Add Export Project Information (#106 @martinburchell)
    • Add Generate Next Record Name (#107 @martinburchell)
    • Add repeat_instance parameter to imp_file request (#104 @martinburchell)
    • Add Delete Record (#77 @damonms)
    • Add Export Reports (#91 @mcarmack)
  • Package Improvements
    • Add redcap_version attribute to Project (#44 Tyler Rivera)
    • Support lazy loading of Projects (#53 Tyler Rivera)
    • Add Python 3 support (#67, #92 @jmillxyz, @fonnesbeck)
    • Remove obsolete Project.filter() (#105 @martinburchell)
    • Change API parameters from comma-separated to arrays (#110 @martinburchell)
    • Use single requests.Session() for connections (#120 @KarthikMasi)
  • Bug Fixes
    • Allow later versions of semantic-version (#108 @martinburchell)
    • Fix package version when installing from GitHub (#113)
    • Handle EmptyData error from pandas read_csv (#118 @martinburchell)
  • Documentation
    • Added REDCap API changelog from 6.0.0 - 6.12.1 (#64 @SlightlyUnorthodox)
    • Python 3 updates (#115 @sujaypatil96)

1.0.2 (2016-10-05)

  • Fix issue in new survey participant export method.

1.0.1 (2016-10-05)

  • Add a Project method to export the survey participant list.
  • Update author email.

1.0 (2014-05-16)

  • Normalize all format argument to default to json, not obj. This better follows the official REDCap API. This breaks backwards compatibility, hence the 1.0 release.
  • Remove the redcap.query and associated tests. If you need filtering functionality, Pandas is highly recommended.
  • Update documentation re: how PyCap implicitly decodes JSON responses.

0.9 (2014-02-27)

  • Update docs about passing CA_BUNDLE through verify_ssl.
  • Canonical URL for docs is now http://pycap.rtfd.org.
  • Add date_format argument for .import_records
  • Sphinxification of docs
  • Add MIT license
  • Add export_survey_fields & export_data_access_groups arguments for .import_records
  • Raise for 5XX responses
  • Raise exception for failed imports
  • Deprecate the entire redcap.Query module. It was a bad idea to begin with.
  • Raise exception during Project instantiation when the metadata call fails. This is usually indicative of bad credentials.

0.8.1 (2013-05-16)

  • By default, in longitudinal projects when exporting records as a data frame, the index will be a MultiIndex of the project’s primary field and redcap_event_name.
  • DataFrames can be passed to Project.import_records.
  • Added Project.export_fem to export Form-Event Mappings from the Project.
  • The SSL certificate on REDCap server can be ignored if need be.

0.8.0 (2013-02-14)

  • Added rest of API methods: Project.export_users, Project.delete_file. Almost
    all API methods are implemented within Project in some way, shape or form.
  • Fix file import bug.
  • Now use relaxed JSON decoding because REDCap doesn’t always send strict JSON.
  • File export, import and delete methods will raise redcap.RedcapError when the
    methods don’t succeed on the server.
  • Low-level content handling has been cleaned up.

0.7.0 (2013-01-18)

  • Added Project.export_file and Project.import_file methods for exporting/ importing files from/to REDCap databases
  • Fixed a dependency issue that would cause new installations to fail
  • Fixed an issue where newline characters in the project’s Data Dictionary would case Projects to fail instantiation.

0.6.1 (2012-11-16)

  • Add ability to alter DataFrame construction with the ‘df_kwargs’ arg in Project.export_records and .export_metadata

0.6 (2012-11-06)

  • Add export_metadata function on redcap.Project class
  • Add ‘df’ as an option for the format argument on the redcap.Project
    export methods to return a pandas.DataFrame

0.5.2 (2012-10-12)

  • Update setup.py for more graceful building

0.5.1 (2012-10-04)

  • Fix potential issue when exporting strange characters

0.5 (2012-09-19)

  • Add initial support for longitudinal databases
  • Add helper attributes on redcap.Project class
  • Improve testing
  • Add Travis-CI testing on github

0.4.2 (2012-03-15)

  • 0.4.1 didn’t play well with pypi?

0.4.1 (2012-03-15)

  • Defend against non-unicode characters in Redcap Project

0.3.4 (2012-01-12)

  • New documentation

0.3.3 (2011-11-21)

  • Bug fix when exporting all fields

0.3.2 (2011-11-21)

  • Works with current version of requests
  • Under-the-hood changes (only json is used for RCRequest)
  • Bug fix in Project.filter

0.3.1 (2011-11-02)

  • Bug fix in import_records

0.3 (2011-09-27)

  • Using Kenneth Reitz’s request module, greatly simplifying request code.

0.21 (2011-09-14)

  • First public release on PyPI
  • Version bump

0.1 (2011-09-14)

  • Basic import, export, metadata

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