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Update repair
command to allow migration of annotation values
#510
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… which to migrate values for deprecated terms. See ontodev#492.
repair
command migrate annotation valuesrepair
command to allow migration of annotation values
This PR addresses @cmungall's request:
However I didn't implement the ALL option. I don't think we would want to accidentally migrate |
@balhoff Thanks for including automated tests. ROBOT will run the integration tests during When just comparing inputs to outputs, I prefer just the integration tests. When comparing different method calls, just the unit tests are better. If that's not clear, we can add better documentation to |
@rctauber suggests that using an option map and resolving the annotation properties inside the operation will make life easier going forward, as more options are added to the command. |
robot-core/src/main/java/org/obolibrary/robot/RepairOperation.java
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Looks good! This covers the case when the subject is obsoleted - for the case when the object is obsoleted, shall we do a separate PR or roll into this one?
@jamesaoverton @rctauber can you say more about what you mean by "option map"? Is there another command that works this way which I can look at? Oh—I think you mean passing a Map structure to the Operation. |
Yes, I think Chris pioneered the use of |
@jamesaoverton @rctauber the method signatures in |
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It looks like properties
is never used.
@balhoff Ok, I'm fine with that. My only remaining comment is that the |
Thanks for catching this! 😬 I fixed that, and also another issue I discovered with |
Thanks @balhoff! |
See #492.
Syntax:
robot repair --input xref-need-of-repair.obo --annotation-property oboInOwl:hasDbXref --output results/xref-repaired.obo