Skip to content
This repository has been archived by the owner on May 23, 2024. It is now read-only.

Replace predicate mapping with a local JSON file #635

Draft
wants to merge 59 commits into
base: master
Choose a base branch
from
Draft

Replace predicate mapping with a local JSON file #635

wants to merge 59 commits into from

Commits on Feb 7, 2023

  1. Added an INNER_LIMIT to prevent queries from stalling.

    @gaurav
    gaurav committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    b33af5a View commit details
    Browse the repository at this point in the history

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

    @gaurav
    gaurav committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    7785a9f View commit details
    Browse the repository at this point in the history

  3. Fixed inner limit.

    @gaurav
    gaurav committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    9cf65d9 View commit details
    Browse the repository at this point in the history

  4. Reduced the inner limit multiplier to 1000.

    @gaurav
    gaurav committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    c872342 View commit details
    Browse the repository at this point in the history

  5. Improved SPARQL code.

    @gaurav
    gaurav committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    045d509 View commit details
    Browse the repository at this point in the history

Commits on Feb 28, 2023

  1. Documented what this new directory is for.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    f04f9eb View commit details
    Browse the repository at this point in the history

  2. GenerateBiolinkPredicateMappings now runs a SPARQL query.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    70834c4 View commit details
    Browse the repository at this point in the history

  3. Added code for retrieving predicate mappings.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    d0672ab View commit details
    Browse the repository at this point in the history

  4. Added transformation code.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    31586e7 View commit details
    Browse the repository at this point in the history

  5. Fixed some syntax issues.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    afdb9bb View commit details
    Browse the repository at this point in the history

  6. Added code to write out the PredicateJsonFilePath.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    853b944 View commit details
    Browse the repository at this point in the history

  7. Added predicates.json to GitHub.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    d5ae7c4 View commit details
    Browse the repository at this point in the history

  8. Moved predicate mapping code into its own class.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    ea49bf7 View commit details
    Browse the repository at this point in the history

  9. First stab at a mapQueryEdgePredicates() method.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    aa420ea View commit details
    Browse the repository at this point in the history

  10. First stab at complete transformation.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    20385b7 View commit details
    Browse the repository at this point in the history

  11. Added reverse operation or something.

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    b685c29 View commit details
    Browse the repository at this point in the history

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

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    157a58d View commit details
    Browse the repository at this point in the history

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

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    d0428d2 View commit details
    Browse the repository at this point in the history

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

    @gaurav
    gaurav committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    b0385ea View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2023

  1. Attempt to improve the Biolink3Test.

    @gaurav
    gaurav committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    f66ee8a View commit details
    Browse the repository at this point in the history

  2. Replaced Biolink predicates code to return all predicates.

    @gaurav
    gaurav committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    9799fe0 View commit details
    Browse the repository at this point in the history

  3. Tests pass, woo.

    @gaurav
    gaurav committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    13bbd54 View commit details
    Browse the repository at this point in the history

Commits on Mar 14, 2023

  1. Updated version for deployment.

    @gaurav
    gaurav committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    c962c9e View commit details
    Browse the repository at this point in the history

  2. Updated two tests to use Biolink3 syntax.

    @gaurav
    gaurav committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    05b97b3 View commit details
    Browse the repository at this point in the history

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

    @gaurav
    gaurav committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    75a8f9e View commit details
    Browse the repository at this point in the history

  4. Added PRCD-increases-chemical example.

    @gaurav
    gaurav committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    92dc566 View commit details
    Browse the repository at this point in the history

  5. Fixed resource loading in predicate mappings.

    @gaurav
    gaurav committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    6f4ecca View commit details
    Browse the repository at this point in the history

Commits on Mar 15, 2023

  1. Added timeout to LookupServiceTest.

    @gaurav
    gaurav committed Mar 15, 2023
    Configuration menu
    Copy the full SHA
    b80ee85 View commit details
    Browse the repository at this point in the history

  2. Removed tests that are timing out (#633). 

    Full link to issue: #633
    @gaurav
    gaurav committed Mar 15, 2023
    Configuration menu
    Copy the full SHA
    d9141a8 View commit details
    Browse the repository at this point in the history

  3. Reformatted files with scalafmtAll.

    @gaurav
    gaurav committed Mar 15, 2023
    Configuration menu
    Copy the full SHA
    e9dd651 View commit details
    Browse the repository at this point in the history

Commits on Mar 17, 2023

  1. Updated LimitTest with updated counts.

    @gaurav
    gaurav committed Mar 17, 2023
    Configuration menu
    Copy the full SHA
    821c7bf View commit details
    Browse the repository at this point in the history

  2. Clarified debugging message and marked it debug().

    @gaurav
    gaurav committed Mar 17, 2023
    Configuration menu
    Copy the full SHA
    0db643d View commit details
    Browse the repository at this point in the history

Commits on Mar 21, 2023

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

    @gaurav
    gaurav committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    7e51c86 View commit details
    Browse the repository at this point in the history

  2. Added manual predicates to match the Biolink3 tests.

    @gaurav
    gaurav committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    cd73b08 View commit details
    Browse the repository at this point in the history

  3. Fixed Biolink3 tests.

    @gaurav
    gaurav committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    96d247e View commit details
    Browse the repository at this point in the history

  4. Manually added downregulates.

    @gaurav
    gaurav committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    08f4127 View commit details
    Browse the repository at this point in the history

  5. Added a test for the KG-result edge name mismatch.

    @gaurav
    gaurav committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    7f97dfa View commit details
    Browse the repository at this point in the history

  6. Fixed KG-results mismatch issue.

    @gaurav
    gaurav committed Mar 21, 2023
    Configuration menu
    Copy the full SHA
    a3e33c6 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2023

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

    @gaurav
    gaurav committed Mar 22, 2023
    Configuration menu
    Copy the full SHA
    c852b75 View commit details
    Browse the repository at this point in the history

Commits on Mar 28, 2023

  1. Incremented Biolink model version to v3.2.2.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    81f9d2c View commit details
    Browse the repository at this point in the history

  2. Improved documentation.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    e08403a View commit details
    Browse the repository at this point in the history

  3. Upgraded to Biolink v3.2.3.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    c48c4bd View commit details
    Browse the repository at this point in the history

  4. Added a QualifiedBiolinkPredicate() type.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    d46edbc View commit details
    Browse the repository at this point in the history

  5. First stab at including QualifiedBiolinkPredicates in Lookup.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    1fb9d44 View commit details
    Browse the repository at this point in the history

  6. Expanded use of QualifiedBiolinkPredicate.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    42d8b45 View commit details
    Browse the repository at this point in the history

  7. Updated tests to use QualifiedBiolinkPredicate.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    d8fee0a View commit details
    Browse the repository at this point in the history

  8. Standardized to qualifiedBiolinkPredicate.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    7796c0f View commit details
    Browse the repository at this point in the history

  9. Standardized to biolinkQualifiedPredicates.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    0796eba View commit details
    Browse the repository at this point in the history

  10. Improved debugging.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    b8cf4a2 View commit details
    Browse the repository at this point in the history

  11. Incremented version number.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    85150b5 View commit details
    Browse the repository at this point in the history

  12. Incremented version.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    6cd40a0 View commit details
    Browse the repository at this point in the history

  13. Incremented version number in build.sbt.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    71d0db6 View commit details
    Browse the repository at this point in the history

  14. Fixed expectations for simple.json.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    2fedd6b View commit details
    Browse the repository at this point in the history

  15. Added two Biolink 3 tests to IT.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    2df9dd3 View commit details
    Browse the repository at this point in the history

  16. Fixed test in ImplicitsTest.

    @gaurav
    gaurav committed Mar 28, 2023
    Configuration menu
    Copy the full SHA
    fc3ada1 View commit details
    Browse the repository at this point in the history

Commits on Apr 1, 2023

  1. Fixed one of the QueryServiceTests by changing the target.

    @gaurav
    gaurav committed Apr 1, 2023
    Configuration menu
    Copy the full SHA
    4e9c6b3 View commit details
    Browse the repository at this point in the history

  2. Fixed identifier for glucose.

    @gaurav
    gaurav committed Apr 1, 2023
    Configuration menu
    Copy the full SHA
    5331039 View commit details
    Browse the repository at this point in the history

  3. Made debugging log explicit.

    @gaurav
    gaurav committed Apr 1, 2023
    Configuration menu
    Copy the full SHA
    a2fd714 View commit details
    Browse the repository at this point in the history

  4. Removed unneeded TODO.

    @gaurav
    gaurav committed Apr 1, 2023
    Configuration menu
    Copy the full SHA
    a9dd2e8 View commit details
    Browse the repository at this point in the history