Define Version reporting

[cfra68]

In the valueset in the odmlib file, only following versions are present: "MetaDataVersion.DefineVersion": ["2.0.0", "2.0", "2.1.0", "2.1"]

When I run the core validation on cdiscpilot01 (datasets and define), it works, but when i change the defineversion in the xml from 2.1.0 to 2.1.5, I got following error:

Traceback (most recent call last):
File "core.py", line 637, in
File "click/core.py", line 1130, in call
File "click/core.py", line 1055, in main
File "click/core.py", line 1657, in invoke
File "click/core.py", line 1404, in invoke
File "click/core.py", line 760, in invoke
File "click/decorators.py", line 26, in new_func
File "core.py", line 273, in validate
File "scripts/run_validation.py", line 186, in run_validation
File "cdisc_rules_engine/services/reporting/excel_report.py", line 111, in write_report
File "cdisc_rules_engine/services/reporting/excel_report.py", line 96, in write_report
File "cdisc_rules_engine/utilities/reporting_utilities.py", line 19, in get_define_version
File "cdisc_rules_engine/services/define_xml/base_define_xml_reader.py", line 349, in get_define_version
File "cdisc_rules_engine/services/define_xml/base_define_xml_reader.py", line 86, in read
cdisc_rules_engine.exceptions.custom_exceptions.FailedSchemaValidation: Unknown value DefineVersion in ValueSet. Unable to check value.
[2990155] Failed to execute script 'core' due to unhandled exception!

Please can new versions be added to the list or can the way of checking be changed?
Thanks.

[JozefAerts]

I would propose that everything that "starts-with" "2.1" is accepted by the engine (besides "2.0" of course)
I just usually use "2.1" for Define-XML version.
Reason is that versions like "2.1.5" are just subversions that have new enumerated terms for some variables.
See e.g. https://www.cdisc.org/standards/foundational/define-xml/define-xml-v2-1
Otherwise it will be a bit hard to keep track of all subversions of Define-XML 2.1 ...

[SFJohnson24]

@cfra68 did you try running with just 2.1 as the define version? Is this still an issue?

[cfra68]

@SFJohnson24 If I try with 2.1 or 2.1.0 I have no issue, but other define versions like 2.1.1, 2.1.2, ... still have the issue (also in prerelase 0.9.2. It would be good that, like suggested by JozefAerts, the validation should check on everything that starts with 2.1.

Our define generation process is following the CDISC Define-XML Specifications Version 2.1, in which the def:DefineVersion attribute has as possible values "2.1.n" where the n in "2.1.n" reflects updates to the schema.

[SFJohnson24]

@cfra68 are you able to run a validation with just the -dxp flag and not the -dv flag. This ticket is going to become deprecating the -dv flag. A lot of engine's define functionality is based on the define itself and I do not believe we actually are using the -dv presently and should move to remove that flag. see here. factory._get_define_xml_reader is calling _from_namespace so it is using the full define version to instantiate the reader. Our reporting is using the defineversion prop and not the namespace so it may report that it is using 2.1 or 2.1.0 version in the report which is a bug we want to address.

A/C for this ticket:

• remove -dv flag. We already get the define_version from the define throughout execution here and here
  version comes from the namespace prop (xmlns:def), not the defineversion prop. I am able to run a test and validate without the -dv flag so I do not believe we are using its functionality at all during validations/tests. Best to make sure though.

• support for minor versions of define: we need to edit get_define_version() as it uses DefineVersion prop and not namespace prop for version in reporting. This is a bug and incorrectly reporting the define version that is being validated. get_define_ct in the reporting also needs to support minor versions.

[cfra68]

@SFJohnson24
I did some extra tests (after changing def:DefineVersion to 2.1.6 in define.xml):

Case 1: Release 081 - with -dv parameter

• C:\Core\RulesEngine081>core validate -d c:/core/cdiscpilot01 -s sdtmig -v 3-3 -dxp c:/core/cdiscpilot01/define.xml -dv 2-1
• result: it looks like the error is occuring after validation, at the moment of creating the excel:

[ERROR 2025-03-10 07:42:35,780 - excel_report.py:110] - Unknown value DefineVersion in ValueSet. Unable to check value.
Traceback (most recent call last):
  File "cdisc_rules_engine\services\define_xml\base_define_xml_reader.py", line 80, in read
  File "odmlib\loader.py", line 28, in MetaDataVersion
  File "odmlib\define_loader.py", line 68, in load_metadataversion
  File "odmlib\define_loader.py", line 25, in load_document
  File "<string>", line 1, in <module>
  File "odmlib\odm_element.py", line 82, in __init__
  File "odmlib\odm_element.py", line 91, in __setattr__
  File "odmlib\typed.py", line 277, in __set__
  File "odmlib\valueset.py", line 78, in value_set
ValueError: Unknown value DefineVersion in ValueSet. Unable to check value.
[22372] Failed to execute script 'core' due to unhandled exception!

Case 2: Release 081 - without -dv parameter

• C:\Core\RulesEngine081>core validate -d c:/core/cdiscpilot01 -s sdtmig -v 3-3 -dxp c:/core/cdiscpilot01/define.xml
• result: same as case 1, so also without -dv flag the error is popping up

Case 3: Release 092 - with -dv parameter

• C:\Core\RulesEngine092>core validate -d c:/core/cdiscpilot01 -s sdtmig -v 3-3 -dxp c:/core/cdiscpilot01/define.xml -dv 2-1
• result: the error is occuring before validation of the rules

Traceback (most recent call last):
  File "core.py", line 834, in <module>
  File "click\core.py", line 1157, in __call__
  File "click\core.py", line 1078, in main
  File "click\core.py", line 1688, in invoke
  File "click\core.py", line 1434, in invoke
  File "click\core.py", line 783, in invoke
  File "click\decorators.py", line 33, in new_func
  File "core.py", line 314, in validate
  File "scripts\run_validation.py", line 126, in run_validation
  File "scripts\script_utils.py", line 105, in get_library_metadata_from_cache
  File "cdisc_rules_engine\services\define_xml\define_xml_reader_2_1.py", line 58, in get_ct_standards_metadata
  File "odmlib\loader.py", line 28, in MetaDataVersion
  File "odmlib\define_loader.py", line 68, in load_metadataversion
  File "odmlib\define_loader.py", line 25, in load_document
  File "<string>", line 1, in <module>
  File "odmlib\odm_element.py", line 82, in __init__
  File "odmlib\odm_element.py", line 91, in __setattr__
  File "odmlib\typed.py", line 277, in __set__
  File "odmlib\valueset.py", line 78, in value_set
ValueError: Unknown value DefineVersion in ValueSet. Unable to check value.
[PYI-22936:ERROR] Failed to execute script 'core' due to unhandled exception!

Case 4: Release 092 - without -dv parameter

• C:\Core\RulesEngine092>core validate -d c:/core/cdiscpilot01 -s sdtmig -v 3-3 -dxp c:/core/cdiscpilot01/define.xml
• result: same as case 3, so also without -dv flag the error is popping up

[SFJohnson24]

@cfra68 thank you for these logs. These will be helpful when this issue is addressed.

[gerrycampion]

This appears to be an issue with odmlib. We will investigate