QC Report branch with test refinement #1428
Conversation
turbomam
commented
Nov 28, 2023
turbomam
commented
- try to fix QC Report PR 1334 in new branch #1427
- expanded use of quality_control_report #1333
turbomam
changed the title
Updating to failed data can have no has_output.
turbomam
changed the title
|
@turbomam I will test that now. |
Removing rule to have has_output be optional if quality_control_report.status=fail
Testing removing invalid data of quality_control_report.status=pass mixed with failure_categorization.
|
@turbomam I need some help getting the mixs.yaml conflicts resolved. |
|
You can delete it from the branch. It gets regenerated by make all, if necessary. Or I can do it in about two hours. |
|
@turbomam the build is failing b/c the example valid data is missing has_output. I thought you were going to add other tests/change how the model was done so this data would pass. |
snakecasing permissible values for FailureWhatEnum
Updating failure_what values to snakecase permissible values
Updating failure_where value to snakecase permissible value.
|
oh yeah. A reasonable solution would be to assert |
Adding quality control slots to PlannedProcess
Adding quality control slots to WorkflowExeuctionActivity
Updates to how quality control slots are modeled
Updates to how quality control information is modeled.
Update example valid data for different quality control modeling.
Updates to modeling for quality control slots
Making qc_failure_what and qc_failure_where multivalued.
rule debugging
Add new test for rule to test that has_output is required if qc_status is not specified.
Test value_presence to enforce rule
Updating to linkml 1.6.6 to fix rule issues.
|
To get the value_presence rules to work correctly I had to update linkml to 1.6.6, then @pkalita-lbl helped identify an issue where rules don't inherit to subclasses. Patrick will make a ticket for the linkml issue, this should be released in early January. Workaround would be to copy rules to each subclass. cc @turbomam @brynnz22 |
|
LinkML issue: linkml/linkml#1802 |
Add comment about permissible values for FailureWhereEnum
Deleting commented out rule
remove having failure_what and failure_where be multivalued, with current modeling failure_categorization is what is multivalued with slots for failure_what and failure_where
