Help with Command Line SEND-AR Validation

[cuppm]

Are examples on how to run validation on a SEND-AR study? I have the latest release - v0.15 downloaded.

I'm using the current command line documentation from the validation --help and what is found here: https://github.com/cdisc-org/cdisc-rules-engine/blob/main/README.md. These have different text displayed, and I'm assuming the README.md version is the most up to date one? But there are different options listed in each.

I'm not entirely sure what to use for the standard, substandard, and version. The README.md documentation has:

  -s, --standard TEXT             CDISC standard to validate against. PRODUCT environment variable can be used to pass value.
                                  [required]
  -v, --version TEXT              Standard version to validate against. VERSION environment variable can be used to pass value.
                                  [required]
  -ss, --substandard TEXT         Substandard to validate against. SUBSTANDARD environment variable can be used to pass value.
                                  "SDTM", "SEND", "ADaM", or "CDASH"
                                  [required for TIG]

I tried this: .\core.exe validate -s sendig-ar -v 1-0 -d "D:\Projects\Study\SEND" -dxp "D:\Projects\Study\SEND\define.xml" -ft xpt
And it output:

Traceback (most recent call last):
  File "core.py", line 938, 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 515, in validate
  File "scripts\run_validation.py", line 139, in run_validation
  File "scripts\script_utils.py", line 142, in get_library_metadata_from_cache
  File "cdisc_rules_engine\services\define_xml\define_xml_reader_2_0.py", line 45, in get_extensible_codelist_mappings
  File "odmlib\loader.py", line 28, in MetaDataVersion
  File "odmlib\define_loader.py", line 68, in load_metadataversion
  File "odmlib\define_loader.py", line 37, in load_document
  File "odmlib\define_loader.py", line 32, in load_document
  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 Type in ValueSet. Unable to check value.
[PYI-86968:ERROR] Failed to execute script 'core' due to unhandled exception!

So I tried running as just SEND 3.1.1 with this command:
.\core.exe validate -s sendig -v 3.1.1 -d "D:\Projects\Study\SEND" -ft xpt -dxp "D:\Projects\Study\SEND\define.xml" -dv 2.0
Which gave me the same error.

This command without specifying a define.xml file did some rule evaluation:
.\core.exe validate -s sendig -v 3.1.1 -d "D:\Projects\Study\SEND" -ft xpt
Note that if I called the core.exe with a path from a different active directory in the command prompt, it would error when trying to write the report because it couldn't find the template file (guessing a path issue).

It appears to run as SEND 3.1.1, but did not auto find the define.xml. And what does NAP mean for substandard and TIG use case? (A non-standard "not applicable" abbreviation?)

I've attached a study data scrubbed version of the report and there are a lot of issues with error/failure status. Some of them can be attributed to the SEND vs SEND-AR and some from not getting extra columns to use as unique from the define.xml.
CORE-Report-2026-04-09T13-16-26 Cleaned.xlsx

The LB dataset label was missing in the Dataset Details tab:

CORE-000455 appears to have a formatting issue with the Variable column population:

The Report Issue Details Row Limit setting (set at 10k) seems to have limited the number of records in the Issue Details tab because VS needs the extra column for record uniqueness from the define.xml. But is there something that limits the number records output per domain/issue so a single repeated issue in a domain doesn't hog the entire feed?

[cuppm]

Update: I retried the -s sendig-ar -v 1.0 option without specifying the define file and it worked.

LB's issue with being read appears to have been a non-ASCII character in the LBMETHOD. The issue was indeed what was in the log file:

I used a hex editor and replaced the 0xe9 (é) values with 0x65 (e) and it was able to be read in by CORE. No other XPT reading software or validation engine chokes on the read for this file, even if non-ASCII characters are not allowed in SEND. Would it be something that could be handled more gracefully in the future with a "non-standard character" check and issue reported for the records it is found in?

Is there a separate location to submit potential rule bugs?

For rules like CORE-000896 I get the issue value:

Failed to execute rule operation. Operation: distinct, Target: POOLID, Domain: POOLDEF, Error: Failed to execute rule operation. Domain POOLDEF does not exist. Operation: distinct, Target: POOLID, Core ID: CORE-000896

I'm assuming these are safe to ignore as the rule doesn't apply if there's no POOLDEF column used, right? So shouldn't this rule's result be hidden like other rules that don't apply because they are for columns not used?

Rule CORE-000529 seems to have an issue in that it's looking for a column name that isn't specified by the IG. There are instances of this rul in my report for AG, DM, DS, EX, SE, SUPPDM, SUPPMA, and SUPPMI:

Failed to execute rule operation. Operation: dy, Target: AGDTC, Domain: AG, Error: 'AGDTC'

Rule CORE-000892 (End timepoint is populated but start timepoint is missing.) for FW seems to be looking for the wrong variable. It lists the variables it's looking at, but FW does not have FWSTDTC it is named FWDTC.

[SFJohnson24]

@cuppm thanks for the detailed write-up and sorry for the delay in response.

1. NAP is not applicable. Substandard and use case are TIG specific. These can be ignored for SEND
   sendig-ar as a standalone standard is not available yet currently for core, you were correct to use just SENDIG. The define.xml needs to be specified using -dxp

But is there something that limits the number records output per domain/issue so a single repeated issue in a domain doesn't hog the entire feed?

2. -mr and -me are our issue limitation commands. -mr limits total issues in the report per execution. -me limits per rule -- see the Readme for in-depth description of this one. -me <limit> True sets a limit per dataset per rule and is what you are looking for (we do not have a way to limit only a single dataset, the limit is enforced on all datasets FYI)

For rules like CORE-000896 I get the issue value:
Failed to execute rule operation. Operation: distinct, Target: POOLID, Domain: POOLDEF, Error: Failed to execute rule operation. Domain POOLDEF does not exist. Operation: distinct, Target: POOLID, Core ID: CORE-000896

3. this is expected behavior as the whole standard was called to run, even rules that are not applicable to submitted data. I created a ticket for this: Feature: silence rules that are not applicable when running a full standard #1722 You can use -er to exclude rules based on CORE-ID

Is there a separate location to submit potential rule bugs?

https://github.com/cdisc-org/cdisc-open-rules is where we have moved the rules to open source them to our users as well as make authoring changes to them in a transparent way. You can go to the Issues tab at the top and submit issues there if you believe some of the rules need to be tweaked and need to be changed. CORE engine repository should be the spot for issues if you believe it is not executing properly at a code level. Your issues with CORE-000529 and CORE-000892 would fall into the former as they are with how the rule is written.

Again, thank you @cuppm for trialing engine.