PyCap 1.1.3
PyCap: Python interface to REDCap
License: MIT

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

.. image:: https://travis-ci.org/redcap-tools/PyCap.svg?branch=master
    :target: https://travis-ci.org/redcap-tools/PyCap
.. image:: https://badge.fury.io/py/PyCap.svg
    :target: https://badge.fury.io/py/PyCap

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 <http://pycap.rtfd.org>`_.

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 :code:`pip`
::

    $ pip install PyCap

Install extra requirements, which allows returning project data as a :code:`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 <https://github.com/jazzband/pip-tools/blob/master/README.rst>`_.
::

    $ 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 <http://pandas.pydata.org>`_ 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 <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