monarch-initiative / monarch-cypher-queries

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Fix unit tests for latest scigraph compatibility #12

Closed kshefchek closed 7 years ago

kshefchek commented 7 years ago

From https://github.com/SciGraph/SciGraph/pull/225#issuecomment-304353081

There were some changes to the way SciGraph parses and stores swagger yaml metadata. It now uses the data modes defined by SwaggerParser instead of custom beans.

We will need to update the tests here: https://github.com/monarch-initiative/monarch-cypher-queries/tree/master/src/test/java/org/monarchinitiative

benwbooth commented 7 years ago

It looks like the broken module, src/test/java/org/monarchinitiative/CypherResources, was written to parse a non-existent yaml file, queries_monarch.yaml, which would have had some swagger 1.0-formatted yaml metadata. That yaml metadata would have been used to drive a test case called diseaseFromPhenotype_test in the CypherQueryTest module. The diseaseFromPhenotype_test is annotated with @Ignore, so will be skipped by the test suite. Its comment reads Example of a test.

It looks like a disabled example test case that was never completed but that depends on SciGraph's obsolete swagger 1.0 data models. I can either remove the test case or comment it out.

kshefchek commented 7 years ago

If it's already being ignored, I vote for commenting it out. We can come back to testing the dynamic queries - many are outdated and should be removed anyway in favor of using biolink.