Schema errors for all datasets reflected in the validation report

[mhungria]

https://github.com/cdisc-org/data-definition-engine/blame/0dce0a58c8c795f560970947c5d485a675e38748/src/define-xml/README.md#L88

define_v_validation_report.xlsx

[swhume]

Which repo did you grab the schema from? The DDE repo or Jeremy's repo?

Is there any more detail on what the issue is? The message in the XLSX report is pretty vague, "Object does not match any allowed schema pattern."

[mhungria]

The DDE, referencing the enclosed define.yaml when cloned the repo.

I executed as follows:
cd /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/src/define-xml
python create_define_json.py
--usdm_file /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/data/protocol/LZZT/usdm/pilot_LLZT_protocol.json
--output_template /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/output/define_v.json
--sdtmct 2025-03-28
--validate define.yaml
--validation_report /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/output/define_v_validation_report.xlsx
--debug

Note: when validating the enclosed schema define.yaml separately, it provided a couple of errors that I tried fixing on my own but got the same results. I noticed a few days later those schema errors were corrected in the tekmeta repo.

Just repeated the test with the tekmeta revised schema, downloaded to the DDE local repo -renamed. Results enclosed - not changed at all:
python create_define_json.py
--usdm_file /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/data/protocol/LZZT/usdm/pilot_LLZT_protocol.json
--output_template /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/output/define_v_t.json
--sdtmct 2025-03-28
--validate define_tekmeta.yaml
--validation_report /Users/marcelinahungria/Documents/W10X1/360i/dde/data-definition-engine/output/define_v_t_validation_report.xlsx
--debug

define_v_t_validation_report.xlsx

[mhungria]

FYI, I made a local adjustment to the create_define_json.py to perform the schema validation with all or any of the 3 methods included in the code (according to user setup), and I am getting some actual problems detected in the report.

Note: for method 3, I iterate over issues.
Example of report:
define_v_t_o_r_just_validation_report.xlsx

We could review at a future meeting when @dostiep is present. I could incorporate it and post it in a branch for team review if you think it could be left as part of the functionality offered.

[mikemolter]

I just responded to this in the team-DDS area in the LinkML Validation issue. As you may know by now, the reason for the somewhat vague error message is because Pierre's program attempts to simplify the validation results. We'll discuss further at the DDS breakout during the 5/28 meeting.

[mhungria]

I'm planning to attend the breakout tomorrow, hopefully I'll be there.

[mikemolter]

Because this issue is also raised in the LinkML Validation issue, I'll close this one.