redcap-toolbox

Python package of REDCap tools

Background

The goal of redcap-toolbox is to provide researchers with the tools to download and upload data to existing REDCap builds. One key aspect of this toolbox is that the minimum number of changes needed to the records are calculated prior to importing data in to REDCap, thereby reducing the API load.

Installing REDCap Toolbox and Supported Versions

redcap-toolbox is available on PyPI:

$ pip install redcap-toolbox

redcap-toolbox officially supports Python 3.8+.

Getting started

redcap-toolbox relies on the environmental variables REDCAP_API_URL and REDCAP_API_TOKEN.

Downloading data

• Download REDCap dataset using download_redcap and provide an output file name. By default, all forms are exported.
• If you want to include survey timestamps, add the optional flag: --survey-fields
• To download specific instrument forms, enter form names to export in a text file, one per line. If in the web UI, the form name has a space in it, replace the space with an underscore. Then, provide that file using the optional flag: --forms get_forms.csv

An example call might look like this:

download_redcap --survey-fields --forms get_forms.csv source_data/full_data.csv

which will download the data set with only the forms defined in the get_forms.csv with timestamps

Downloading reports

• Reports can be downloaded using download_redcap_report with either a list of report IDs separated by commas or a file with list of report IDs, one per line.
• Use the --prefix flag, to specify the prefix to be added for the filenames. Default is redcap.

An example call might look like this:

download_redcap_report --file report_ids.csv --prefix StudyName report_data

or

download_redcap_report --id 32001,32004 --prefix StudyName report_data

which will save all the reports for IDs listed in the report_ids.csv file in the report_data directory.

• The output report filenames will look like this:

  report_data
  ├── StudyName__report_32001.csv
  └── StudyName__report_32004.csv
  

Splitting REDCap data into event files

• Use split_redcap_data to split the REDCap CSV file into:

  • A file for each event
  • A file for repeated instruments in events where they happen

• So, if your data has events 'scr', 'pre', and 'post', and 'pre' and 'post' each have a repeated instrument called 'meds', you can expect the output files to like this:

  ├── redcap__scr.csv
  ├── redcap__pre.csv
  ├── redcap__pre__meds.csv
  ├── redcap__post.csv
  ├── redcap__post.csv
  └── redcap__post__meds.csv
  

• In addition, if you don't like the whole _arm_1 appended to your event names (who does like that?) or you're using events to denote arms and want all your event's data together, you can use the event_map file for this. That file should be a CSV file and contain the columns 'redcap_event' and 'filename_event'

  • Example event maps might look like:

    scr__all_arm_1,scr
    pre__control_arm_1,pre
    pre__intervention_arm_1,pre
    

An example call might look like this:

split_redcap_data --event-map=event_map.csv --prefix StudyName --no-condense source_data/full_data.csv source_data

where the split event files will be saved in the source_data directory as well with the prefix StudyName added to them.

source_data
├── full_data.csv
├── StudyName__scr.csv
├── StudyName__pre.csv
├── StudyName__pre_meds.csv
├── StudyName__post.csv
└── StudyName__post_meds.csv

Update records in REDCap

• Update the REDCap database with the minimum changes needed to make the system in sync.
• It is important that the updated data file has the same number of rows and columns as the original data file.
• This functionality is especially useful when updating the record information for Tracking purposes.

An example call might look like this:

update_redcap_diff StudyName__scr.csv StudyName__scr_cache.csv

where the _cache.csv file contains the changes made to the original data file.

Credits

redcap-toolbox was written by Nate Vack [email protected], with features added by Nicholas Vanhaute [email protected] and Stuti Shrivastava [email protected]. redcap-toolbox is copyright 2023 by the Boards of Regents of the University of Wisconsin System.