Bug: extract_logged_cda_to_csv_by_zip.sh does not populate several CSV columns

Summary

Running the Bash script extract_logged_cda_to_csv_by_zip.sh against the 14-day Wolfsburg sample placed on the fileshare produces a CSV whose header lists all required AKTIN / DIVI fields, yet several columns are always NA.

Screenshots provided by Dr. Jennifer Kreklow show the empty fields highlighted in yellow (see cedis_mts_transfer.png & docid_case_diag.png).

This blocks QA and prevents starting the full export.

Affected columns

Steps to reproduce

1. 
   

   Request two real-world test CDAs from IT (see Contact below) that contain non-empty values for the affected fields.

   
   


2. 
   

   Place the CDAs in a directory, e.g. /share/cda_test/.

   
   


3. 
   

   Run the script:
   
   ./extract_logged_cda_to_csv_by_zip.sh /path/to/aktin.properties /share/cda_test/

   
   


4. 
   

   Open the generated cda_data_<timestamp>.csv and verify that the columns listed above are still NA.

   
   

Environment

• 
  

  Script version 1.1 (10 Oct 2024)

  
  


• 
  

  Bash 5.2, Debian 12 container (same behaviour on RHEL 9)

  
  


• 
  

  aktin.properties from Wolfsburg deployment (encounter & billing roots verified)

  
  

Contact

• 
  

  Tomasz Babiuch – (please provide two representative CDA files covering the missing fields)

  
  


• 
  

  CC: Robert Dietrichs, Dr. Jennifer Kreklow

  
  

Analysis / Suspected root causes

1. 
   

   Incorrect root IDs – The encounter_root and billing_root values in aktin.properties may not match the IDs actually used in the test CDAs.

   
   


2. 
   

   Regex too strict – Current grep patterns require an explicit xsi:type prefix and may not allow namespace variations.

   
   


3. 
   

   Multiple occurrences – Using head -1 might pick the wrong section (e.g. administrative vs. clinical) where the field is genuinely empty.

   
   

Proposed fix

• 
  

  Generalise regex patterns to accept optional namespace prefixes and whitespace.

  
  


• 
  

  Validate root IDs by echoing them in the log; abort with a clear error if not found.

  
  


• 
  

  Add a helper script / unit test that parses a mini-CDA snippet for each field.

  
  


• 
  

  Emit a warning whenever a header field resolves to NA but the tag exists elsewhere in the file (helps QA).