New duplicate_exact_synonym test in robot report does not display values

[allenbaron]

In robot report, the updated duplicate_exact_synonym test does not display the values for the ?entity ?property ?value triples.

Examples:
Mondo OBO dashboard output - http://dashboard.obofoundry.org/dashboard/mondo/robot_report.html

DO using ROBOT 1.9.6

Note that this has a value for duplicate_label_synonym test.

Using the query at https://github.com/ontodev/robot/blob/master/robot-core/src/main/resources/report_queries/duplicate_exact_synonym.rq in robot query does include the values. In the test I did with DO, it also returned an additional row -- one class had synonyms matching two other classes, so that class appeared twice in the output that contained values and only once in the robot report output (in each case only distinct outputs were retained).

[matentzn]

@allenbaron thanks for detecting this! Any chance you might be willing to fix it? Maybe with the help of ChatGPT :D Sorry for asking but straaaaaapppped for ROBOT dev time!

[allenbaron]

I'll see what I can do.

[allenbaron]

Okay, for 1.9.6... when I run the robot report with a profile limiting to just duplicate_exact_synonym I get 17 results and the values column is empty using doid-edit.owl (same as the full report), repeating this error.

Command

robot report -i doid-edit.owl --profile profile.txt -o DEL.tsv

Where profile.txt has this:

WARN	duplicate_exact_synonym

Output: 17 results, no values

Level	Rule Name	Subject	Property	Value
WARN	duplicate_exact_synonym	DOID:0050035	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:14095	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0070475	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:4464	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0110861	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:898	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:2477	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:683	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0040101	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0040102	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0050156	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0060941	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0050541	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0070042	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:1925	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:0110957	oboInOwl:hasExactSynonym	
WARN	duplicate_exact_synonym	DOID:1926	oboInOwl:hasExactSynonym	

---

The error is eliminated if I copy the exact query from the robot repository and switch the profile to this file: input. In this case, there are 18 results and the values are present in the output (matching the use of robot query).

robot report -i doid-edit.owl --profile profile-file.txt -o DEL.tsv

Where profile-file.txt has this:

WARN	file:./duplicate_exact_synonym.rq

Output: 18 results, has values

Level	Rule Name	Subject	Property	Value
WARN	duplicate_exact_synonym	DOID:0050035	oboInOwl:hasExactSynonym	south african tick-bite fever@en
WARN	duplicate_exact_synonym	DOID:14095	oboInOwl:hasExactSynonym	South African tick-bite fever@en
WARN	duplicate_exact_synonym	DOID:0070475	oboInOwl:hasExactSynonym	renal medullary carcinoma@en
WARN	duplicate_exact_synonym	DOID:4464	oboInOwl:hasExactSynonym	renal Medullary carcinoma@en
WARN	duplicate_exact_synonym	DOID:0110861	oboInOwl:hasExactSynonym	Polycystic Kidney and Hepatic Disease 1@en
WARN	duplicate_exact_synonym	DOID:898	oboInOwl:hasExactSynonym	POLYCYSTIC KIDNEY AND HEPATIC DISEASE 1@en
WARN	duplicate_exact_synonym	DOID:2477	oboInOwl:hasExactSynonym	Peripheral Motor Neuropathy@en
WARN	duplicate_exact_synonym	DOID:683	oboInOwl:hasExactSynonym	peripheral motor neuropathy@en
WARN	duplicate_exact_synonym	DOID:0040101	oboInOwl:hasExactSynonym	neoprene allergy@en
WARN	duplicate_exact_synonym	DOID:0040102	oboInOwl:hasExactSynonym	neoprene allergy@en
WARN	duplicate_exact_synonym	DOID:0050156	oboInOwl:hasExactSynonym	idiopathic pulmonary fibrosis@en
WARN	duplicate_exact_synonym	DOID:0060941	oboInOwl:hasExactSynonym	Idiopathic pulmonary fibrosis@en
WARN	duplicate_exact_synonym	DOID:0050541	oboInOwl:hasExactSynonym	hereditary motor and sensory neuropathy@en
WARN	duplicate_exact_synonym	DOID:2477	oboInOwl:hasExactSynonym	Hereditary motor and sensory neuropathy@en
WARN	duplicate_exact_synonym	DOID:0070042	oboInOwl:hasExactSynonym	fifth digit syndrome@en
WARN	duplicate_exact_synonym	DOID:1925	oboInOwl:hasExactSynonym	Fifth Digit Syndrome@en
WARN	duplicate_exact_synonym	DOID:0110957	oboInOwl:hasExactSynonym	Acid Beta-Glucosidase Deficiency@en
WARN	duplicate_exact_synonym	DOID:1926	oboInOwl:hasExactSynonym	acid beta-glucosidase deficiency@en

[allenbaron]

Last week I was able to get a debugger running in VS code from a FORK of the robot repository and these two commands/profiles reliably returned the same results. I had to stop debugging after only a little while.

When I came back to my debugging set up this week and ran these two tests, they now both return 18 results with values. In fact, running the full report works in my debugging setup now and I did not change any of the code.

This is the command that the debugger in VS code runs.

cd /Users/allenbaron/Documents/FORKS/robot ; 
/usr/bin/env /Library/Java/JavaVirtualMachines/jdk-11.0.17.jdk/Contents/Home/bin/java 
  -agentlib:jdwp=transport=dt_socket,server=n,suspend=y,address=localhost:55778
  @/var/folders/75/42gycvd5371d067rsj3tmv6c0000gp/T/cp_vlh8qeu59vgztfwz496d3ymn.argfile
  org.obolibrary.robot.CommandLineInterface report -i doid-edit.owl -o DEL3.tsv 

I have no idea what happened.

[matentzn]

So with a newly downloaded robot 1.9.6, you get the synonym values correctly?

[allenbaron]

No that still doesn't work. It just works in my debugging setup. I tried mvn clean package to see if some magic happened I was unaware of and the resulting robot.jar also still has the error. Really annoying.

[jamesaoverton]

I can reproduce this using the 1.9.6 robot.jar, running java -jar robot.jar report -i doid-edit.owl --profile profile.txt -o DEL.tsv against a checkout of Disease Ontology main branch.

1. when profile.txt contains WARN duplicate_exact_synonym I get 15 results with nothing in the Vale column
2. when profile.txt contains WARN file:./duplicate_exact_synonym.rq pointing to a copy of robot-core/src/main/resources/report_queries/duplicate_exact_synonym.rq I get 16 results with labels in the Value column

I have no idea what the relevant difference is.