experiment/src/org/labkey/experiment/samples/SampleTypeFolderWriter.java:106

• The comment states "only want the sample derivation runs" but the implementation also includes aliquot runs (SAMPLE_ALIQUOT_PROTOCOL_LSID). Consider updating the comment to clarify that both derivation and aliquot protocol runs are included.

        // only want the sample derivation runs; other runs will get included in the experiment xar.

api/src/org/labkey/api/exp/api/ExperimentService.java:811

• The JavaDoc comment could be more detailed. Consider expanding it to explain: (1) what "derivation run IDs" means in this context, (2) that it includes runs where materials from the specified sample types are used as either inputs or outputs, (3) the behavior of the includeRunsWithDataIO parameter more explicitly (when true, includes all derivation and aliquot runs; when false, includes aliquot runs and only derivation runs without data inputs/outputs).

    /** Get derivation/aliquot run IDs for sample types — filtered by protocol and optionally excluding runs with data inputs/outputs */
    List<Long> getDerivationRunIdsForSampleTypesExport(Collection<String> sampleTypeLsids, Container c, boolean includeRunsWithDataIO);

api/src/org/labkey/api/exp/api/ExperimentService.java:808

• The JavaDoc comment could be more detailed. Consider expanding it to explain: (1) that it returns run IDs where the specified data class is used as either input or output, (2) that it only includes runs with the SAMPLE_DERIVATION_PROTOCOL that have no material inputs or outputs (since those are handled by the sample type writer).

    /** Get derivation run IDs for a data class — runs with SAMPLE_DERIVATION_PROTOCOL that have no material inputs/outputs */
    List<Long> getDerivationRunIdsForDataClassExport(long dataClassRowId);