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PyCap: Python interface to REDCap

Project description

**I am no longer actively developing this code base. Please continue to submit bugs and I'll do my best to tackle them.**

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PyCap is a python module exposing the REDCap API through some helpful abstractions. Information about the REDCap project can be found at

Available under the MIT license.


Canonical documentation can be found on `ReadTheDocs <>`_.


Currently, these API calls are available:

- Export Records
- Export Metadata
- Import Records
- Export File
- Import File
- Delete File
- Export Users
- Export Form Event Mappings

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


- requests (>= 1.0.0)

``$ pip install requests``


>>> 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
>>> 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

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


$ git clone git:// PyCap
$ cd PyCap
$ python install


$ pip install PyCap


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 doi:10.5281/zenodo.9917


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 ` <>`_.
* Add ``date_format`` argument for ``.import_records``
* Sphinxification of docs
* Add MIT license
* Add ``export_survey_fields`` & ``export_data_access_groups`` arguments for
* 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 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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