dwh-scripts/extract_logged_cda_to_csv_by_zip.sh does not work sufficiently

[jonasbienzeisler]

Bug: extract_logged_cda_to_csv_by_zip.sh does not populate several CSV columns

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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.

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Affected columns

CSV column | Expected CDA element / CodeSystem | Current value | Notes -- | -- | -- | -- CEDIS Code | | NA | all rows MTS Score | | NA | all rows Transfer | | NA | all rows Discharge Code | | NA | all rows Document ID | | NA | all rows Internal Case Nr. | | NA | all rows Diagnosis | | NA | all rows

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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.

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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)

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Contact

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

• CC: Robert Dietrichs, Dr. Jennifer Kreklow

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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.

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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).