1.8.2 breaks dashboard

[matentzn]

Unfortunately I cannot debug this before end of the month, but this is the symptoms:

ROBOT 1.8.1 works normal
ROBOT 1.8.2 causes this exception in the dashboard:

-----------------
Checking proco
Running ROBOT report on proco...
profile.txt
ERROR: unable to run check 6 for proco
CAUSE:
An error occurred while calling o6.getViolationCount.
: java.lang.Exception: \'duplicate_definition\' is not a rule in this Report
\tat org.obolibrary.robot.checks.Report.getViolationCount(Report.java:587)
\tat java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
\tat java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)
\tat py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
\tat py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
\tat py4j.Gateway.invoke(Gateway.java:282)
\tat py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
\tat py4j.commands.CallCommand.execute(CallCommand.java:79)
\tat py4j.GatewayConnection.run(GatewayConnection.java:238)
\tat java.base/java.lang.Thread.run(Thread.java:829)

ERROR: unable to run check 12 for proco
CAUSE:
An error occurred while calling o6.getViolationCount.
: java.lang.Exception: \'duplicate_label\' is not a rule in this Report
\tat org.obolibrary.robot.checks.Report.getViolationCount(Report.java:587)
\tat java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
\tat java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)
\tat py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
\tat py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
\tat py4j.Gateway.invoke(Gateway.java:282)
\tat py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
\tat py4j.commands.CallCommand.execute(CallCommand.java:79)
\tat py4j.GatewayConnection.run(GatewayConnection.java:238)
\tat java.base/java.lang.Thread.run(Thread.java:829)

Its not major major for me because I can use the old ODK for now, but maybe this needs looking at?

[jamesaoverton]

Thanks @matentzn. @beckyjackson can you please look into this? It seems suspiciously similar to #943.

[beckyjackson]

@matentzn could you point me to the file for proco? I'm not seeing it as part of OBO Foundry.

[matentzn]

The error happens for all ontologies, I noticed it only this morning when refreshing https://github.com/OBOFoundry/obo-nor.github.io

https://github.com/OBOFoundry/obo-nor.github.io/blob/master/dashboard-config.yml#L7

This will be very hard to test unfortunately. I think the easiest would be to create a little notebook that recreates this line:

https://github.com/OBOFoundry/OBO-Dashboard/blob/master/util/dashboard/dashboard.py#L173

[beckyjackson]

This update here is what's causing the problem - #879

We're now using these ReportQuery objects instead of the old maps that contained rule name -> violations. I deprecated the functions and thought backwards compatibility was OK, but since these maps don't get updated, when you call getViolationCount() on a report, it doesn't have anything to return. I'm going to make a PR to fix the backwards compatibility. This function is currently deprecated but it shouldn't be, because it's still useful for ROBOT as a library.