pycap 1.1.3

PyCap: Python interface to REDCap

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

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