Changing createNeighbors to omit redundant genus in equivalence axiom…

[cmungall]

…, see geneontology/amigo#360

[kltm]

@cmungall I'm still getting three parents for GO:1902401.

[cmungall]

Note that previously tests were failing, meaning `mvn clean install` wouldn't have made a new jar. The tests were failing as they were overfitting for the case we now want to avoid. Fixed tests coming up as soon as I'm off BART...

…

On 10 Mar 2017, at 18:21, kltm wrote: kltm requested changes on this pull request. @cmungall I'm still getting three parents for GO:1902401. -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #177 (review)

[cmungall]

odd, 2490d2c should have failed.

[cmungall]

Add a test explicitly for

[Term]
id: GO:1902401
name: detection of stimulus involved in mitotic DNA damage checkpoint
namespace: biological_process
def: "Any detection of stimulus that is involved in mitotic DNA damage checkpoint." [GOC:mtg_cell_cycle, GOC:TermGenie]
synonym: "perception of stimulus involved in mitotic DNA damage checkpoint" RELATED [GOC:TermGenie]
synonym: "stimulus detection involved in mitotic DNA damage checkpoint" EXACT [GOC:TermGenie]
synonym: "stimulus sensing involved in mitotic DNA damage checkpoint" RELATED [GOC:TermGenie]
is_a: GO:0072400 ! detection of stimulus involved in mitotic DNA integrity checkpoint
intersection_of: GO:0051606 ! detection of stimulus
intersection_of: part_of GO:0044773 ! mitotic DNA damage checkpoint
created_by: jl
creation_date: 2013-09-12T12:07:12Z

[kltm]

Are the tests now catching this?

[cmungall]

Yes:

owltools/OWLTools-Core/src/test/java/owltools/graph/OWLGraphWrapperEdgesAdvancedTest.java

Line 151 in 46ba478

assertFalse(neighbors.hasEdge(new OWLShuntEdge("GO:1902401", "GO:0051606", "is_a")));

so the code is functioning as expected, and does not include the redundant genus term

[kltm]

So the test is passing (with a cut down ontology load?), but my loads still have the errant third edge? Hm.
Is there any way to prosecute owltools about where the edge is coming from on the cli?

[cmungall]

not sure what you mean about the cli query...

[kltm]

Just trying to find a way to test/probe it without having to load the full ontology set.

[cmungall]

I find it easiest to do ad-hoc tests using--solr-url mock, which will create a Mock solr loader (emits json)