Redcap sample data convert to data model V3

[rjiang9]

Hi Marion, @mshadbolt

I wonder whether you can share a sample REDCap raw data file that work with your script of https://github.com/CanDIG/clinical_ETL_code/blob/mshadbolt/add-v3-redcap/sample_inputs/redcapv3_example/preprocess_redcap_data.py

The data I am working on were kind of exported from REDCap (fake data sample attached) but in previous version of Data model (not in V3).

1. Raw & Label data:
   fake-labels.csv
   fake-raw.csv

2. splitted files by schema:
   splited-data.zip

When I ran the CSVConvert on the data, I ran into quite few issues.

3. My redcap2moh.csv
4. My manifest.yml

description:  The mappings of REDCap datat to MoHpackets format for katsu
mapping: redcap2moh.csv
identifier: submitter_donor_id
schema:   https://raw.githubusercontent.com/CanDIG/katsu/develop/chord_metadata_service/mohpackets/docs/schemas/schema.yml
schema_class: MoHSchemaV3
reference_date: earliest_date(singleton.date_resolution, primary_diagnosis.date_of_diagnosis)
date_format: YMD
functions:
    - redcap

I appreciate it very much if you can take a quick look and see if I have done some parts of it wrongly.

Best,
Ray

[mshadbolt]

Hi Ray, can you elaborate on what you mean by the issues on CSVConvert. Is it failing to run at all? Does it give an error message? Or does it run and then you get a lot validation errors?

[rjiang9]

Hi Ray, can you elaborate on what you mean by the issues on CSVConvert. Is it failing to run at all? Does it give an error message? Or does it run and then you get a lot validation errors?

I will get back later, Marion. Thanks