Issue 48298: Align API Filter Operators

[RosalineP]

Rationale

In the process of adding lineage filter operators to the APIs, I noticed a handful of inconsistencies I'm resolving across the APIs. See related pull requests.

Related Pull Requests

• Issue 48298: Align API Filter Operators labkey-api-python#61
• Issue 48298: Align API Filter Operators labkey-api-js#157
• Issue 48298: Align API Filter Operators labkey-api-r#95
• Issue 48298: Align API Filter Operators #60

Changes

• Update Changelog
• Update comments
• Add the following operators:
  • ONTOLOGY_IN_SUBTREE
  • ONTOLOGY_NOT_IN_SUBTREE
  • EXP_CHILD_OF
  • EXP_PARENT_OF
  • EXP_LINEAGE_OF

[RosalineP]

Manual Test Plan

• Lineage Filter Operators

  • Go into a SM folder
  • Create a sample type with no manually added fields
  • Create three samples, accepting defaults. Choose one of them (say it's S-3) and click 'Aliquot Selected', choosing two Aliquots per Parent, and accepting defaults for aliquot creation
  • Go to /query-executeQuery.view?schemaName=sampleManagement&query.queryName=SourceSamples and add the LSID column
  • QueryFilter.Types.EXP_LINEAGE_OF:
    • Using the Java api, execute a selectRows against sampleManagement.SourceSamples, with a filter containing the components:
      • column: "lsid"
      • value: "{json:[<LSID of S-3>,10]}"
      • filter operator: EXP_LINEAGE_OF
    • Verify results:
      • S-3-1
      • S-3-2
  • QueryFilter.Types.EXP_CHILD_OF:
    • Using the Java api, execute a selectRows against samples.<Sample Type Name>, with a filter containing the components:
      • column: "lsid"
      • value: "<LSID of S-3>"
      • filter operator: EXP_CHILD_OF
    • Verify results:
      • S-3-2
      • S-3-1
  • QueryFilter.Types.EXP_PARENT_OF:
    • Using the Java api, execute a selectRows against samples.<Sample Type Name>, with a filter containing the components:
      • column: "lsid"
      • value: "<LSID of S-3-1>"
      • filter operator: EXP_PARENT_OF
    • Verify results:
      • S-3

• Ontology Filter Operators

  • Load NCIT sample ontology from ontologies repo test/sampledata/ontology/owl/Thesaurus.owl/ncit.zip
  • Execute code like the following:

            SelectRowsCommand cmd = new SelectRowsCommand("ontology", "concepts");
            cmd.setColumns(Arrays.asList("Label", "Code", "Metadata", "Description", "OntologyId"));
            cmd.setFilters(List.of(new Filter("Code", "NCIT:C50367" /* Bed */, Filter.Operator.ONTOLOGY_IN_SUBTREE)));
            SelectRowsResponse response = cmd.execute(cn, "/Shared");
            System.out.println("Number of rows: " + response.getRowCount());
            response.getRows().stream().limit(10).forEach(System.out::println);

• This should result in three rows, the parent "bed" concept plus its two children, "Specialty Bed" and "Scanner Patient Bed"
• Replace ONTOLOGY_IN_SUBTREE with ONTOLOGY_NOT_IN_SUBTREE and it should indicate 160,423 rows (total rows 160,426 less the three "bed" concepts)

[labkey-adam]

Code looks good. I'll do manual testing later today.

[labkey-adam]

Manual testing complete. I added an example for the ontology filters to your comment above.