Class SampleToBioSourceTransformer

  • All Implemented Interfaces:
    SourceItemTransformer

    public class SampleToBioSourceTransformer
    extends AbstractSourceItemTransformer
    Source item transformer that transform sample items to their parent biosources. This implementation will only transform to the sample:s immediate parent biosources. Grandparents are not included. To do this, combine this transformer with a SampleToParentSampleTransformer.
    Since:
    3.5
    Author:
    Nicklas
    • Field Detail

      • pushOnly

        private boolean pushOnly
    • Constructor Detail

      • SampleToBioSourceTransformer

        public SampleToBioSourceTransformer()
      • SampleToBioSourceTransformer

        public SampleToBioSourceTransformer​(boolean childrensThatPushOnly)
        Create a new sample to biosource transformer that only load parent biosources to sample that has a subtype with "push annotations" set. This functionality should only be used in the first transformation step.
        Since:
        3.16
        See Also:
        PushToParentsTransformer
    • Method Detail

      • transform

        public Set<Integer> transform​(TransformContext context,
                                      Set<Integer> source)
        Load the ID of all biosources that are immediate parents to the given set of samples.