Incorporate HEAL CDE team labels export directly into KGX export

[gaurav]

Every month, the HEAL CDE team automatically e-mails us an export from their REDCap questionnaire that they use to ask studies about which CRFs each study plans to use. We should make it as easy as possible to incorporate that information into the pipeline provided in this repository. This will require three steps:

Step 1. Extracting mappings from the export ("labels") file

The export ("labels") file is a CSV file with an odd structure:

• The Record ID field will tell you when a study provided information on multiple measures.
• The first row with a particular Record ID field contains the study information, including:
  • PI First and Last Name, e-mail, phone number
  • Project number
  • Project title
  • HEAL Research Program
  • Estimated study enrollment
  • Adult/Pediatric
  • Chronic/Acute pain
  • Columns for the core CRFs: Adult Demographics, PEG (for chronic pain), etc.
  • Will your study be using Spanish-language/other language CRFs?
  • How does your study intend to monitor opioid use?
  • Complete? -- not really useful to us but good to know
  • Survey Timestamp
• For custom mappings, there are additional rows for each measure (with the same Record ID to tie things together), which uses:
  • Name of Measure
  • Name of Other Measure
  • Please include any translated versions of the Case Report Form(s) (CRF) in languages other than English, if applicable: (these are attachments, I suppose)
  • Measure Name
  • Domain
  • Measure Start Date
  • Measure End Date
  • Complete?
  • Please attach the license or permission for this Copyrighted measure.

Naturally this export will change if the input file changes, so having one Python script that handles this transform with minimal configuration and fails fast is probably the best idea. I anticipate that it will produce three outputs:

1. A studies.json file that has information from studies (identified by the project identifier) to the
2. A measures.json file that describes each measure, but grouping study identifiers.

Step 2. Harmonize

TODO

Step 3. Produce KGX files.

TODO