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Generate test data with qualifiers #640

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Generate test data with qualifiers #640

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Commits on Feb 7, 2023

  1. Added an INNER_LIMIT to prevent queries from stalling.

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  2. Increased the inner limit based on the outer limit value.

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  3. Fixed inner limit.

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  4. Reduced the inner limit multiplier to 1000.

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  5. Improved SPARQL code.

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Commits on Feb 28, 2023

  1. Documented what this new directory is for.

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  2. GenerateBiolinkPredicateMappings now runs a SPARQL query.

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  3. Added code for retrieving predicate mappings.

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  4. Added transformation code.

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  5. Fixed some syntax issues.

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  6. Added code to write out the PredicateJsonFilePath.

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  7. Added predicates.json to GitHub.

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  8. Moved predicate mapping code into its own class.

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  9. First stab at a mapQueryEdgePredicates() method.

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  10. First stab at complete transformation.

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  11. Added reverse operation or something.

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  12. Merge branch 'fix-query-stalling' into replace-predicate-mapping

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  13. Added hacky checks to make sure predicates.json doesn't exist.

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  14. Added Biolink3Test, changed some behavior, noted a needed fix.

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Commits on Mar 7, 2023

  1. Attempt to improve the Biolink3Test.

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  2. Replaced Biolink predicates code to return all predicates.

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  3. Tests pass, woo.

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Commits on Mar 14, 2023

  1. Updated version for deployment.

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  2. Updated two tests to use Biolink3 syntax.

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  3. Updated Biolink 3 example queries with results we can understand.

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  4. Added PRCD-increases-chemical example.

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  5. Fixed resource loading in predicate mappings.

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Commits on Mar 15, 2023

  1. Added timeout to LookupServiceTest.

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    gaurav committed Mar 15, 2023
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  2. Removed tests that are timing out (#633). 

    Full link to issue: #633
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    gaurav committed Mar 15, 2023
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  3. Reformatted files with scalafmtAll.

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    gaurav committed Mar 15, 2023
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Commits on Mar 17, 2023

  1. Updated LimitTest with updated counts.

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    gaurav committed Mar 17, 2023
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  2. Clarified debugging message and marked it debug().

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    gaurav committed Mar 17, 2023
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Commits on Mar 21, 2023

  1. Fixed TRAPITest tests (by checking for unmapped predicates).

    @gaurav
    gaurav committed Mar 21, 2023
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  2. Added manual predicates to match the Biolink3 tests.

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    gaurav committed Mar 21, 2023
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  3. Fixed Biolink3 tests.

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    gaurav committed Mar 21, 2023
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  4. Manually added downregulates.

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    gaurav committed Mar 21, 2023
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  5. Added a test for the KG-result edge name mismatch.

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    gaurav committed Mar 21, 2023
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  6. Fixed KG-results mismatch issue.

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    gaurav committed Mar 21, 2023
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Commits on Mar 22, 2023

  1. Various attempts at figuring out why the query_id isn't working.

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    gaurav committed Mar 22, 2023
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Commits on Mar 28, 2023

  1. Incremented Biolink model version to v3.2.2.

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  2. Improved documentation.

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  3. Upgraded to Biolink v3.2.3.

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  4. Added a QualifiedBiolinkPredicate() type.

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  5. First stab at including QualifiedBiolinkPredicates in Lookup.

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  6. Expanded use of QualifiedBiolinkPredicate.

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  7. Updated tests to use QualifiedBiolinkPredicate.

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  8. Standardized to qualifiedBiolinkPredicate.

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  9. Standardized to biolinkQualifiedPredicates.

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  10. Improved debugging.

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  11. Incremented version number.

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  12. First stab at a GenerateTestData utility.

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  13. Making progress.

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  14. Okay, so now we're querying test data.

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  15. First stab at a TestEdge generator.

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  16. Fixed bug.

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  17. Turned off sorting.

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  18. First stab at a test-edges file.

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  19. Updated test edges; trying to catch error didn't work.

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  20. Completed running the test-edges.jsonl file.

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  21. Larger test edges output.

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  22. Regenerated test-edges.jsonl.

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  23. Reformatted code with scalafmtAll.

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  24. Re-ran test edge generation.

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  25. First stab at an SRI testing file.

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  26. Updated GenerateTestData to generate an SRI Testing file. 

    In the format specified at https:/TranslatorSRI/SRI_testing/blob/83358cb18bdebd5a45b8f4c4671cb027328df700/tests/onehop/README.md#configuring-the-tests
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  27. Uniquified the test data.

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  28. Added test_data_location to Server metadata.

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Commits on Apr 1, 2023

  1. First stab at writing out test data with qualifiers. 

    We should now have everything we need to make this work. Unfortunately,
of course, it doesn't. So now we need to figure out why.
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Commits on Apr 25, 2023

  1. Filtered out non-leaf Biolink classes.

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Commits on May 2, 2023

  1. Fixed code for generating test data.

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  2. Reorganized and improved code.

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  3. Added code for translating relations into biolink predicates.

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  4. Improved error output.

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  5. Fixed bug and output.

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  6. Fixed bugs in logic and filtering.

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  7. Uniquified test edges (up to a point).

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  8. Consistently use shorthand IRIs for everything.

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  9. Added a check to prevent tests with the same subject and object.

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  10. Took out the tip-only filter.

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  11. Improved imports.

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