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Gemma2 compat - #60
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Gemma 2.0 renamed four fields on the annotation value object
(Gemma b5c6747f68, live on gemma2.msl.ubc.ca):
className -> category termName -> value
classUri -> categoryUri termUri -> valueUri
There are no aliases: gemma.msl.ubc.ca (1.32.x) serves only the old
spelling, gemma2.msl.ubc.ca only the new one. Verified by fetching
/datasets/1/annotations from both.
The result reads BOTH. gemmaPath() still defaults to
https://gemma.msl.ubc.ca/rest/v2/ and tests/testthat.R pins
setGemmaPath('prod'), so a Gemma 2 server is reached only by setting
options(gemma.API=...); a hard switch would blank the columns against
the default target and take the suite with it. accessRenamedField()
picks the spelling the payload actually carries, per field, per
response, and can be deleted when gemma.R drops Gemma 1.x.
Released gemma.R is unaffected -- it targets Gemma 1.0, which still
serves the old names.
The package's own columns do not move: class.name, class.URI,
term.name and term.URI keep their names and only change which wire
field they read. Whether gemma.R adopts category/value is a separate
decision for a major version.
processAnnotations, behind get_dataset_annotations, is the only reader
affected. processSearchAnnotations (search_annotations,
get_annotation_children, get_annotation_parents) and
processCharacteristicValueObject (sample.characteristics) already read
category/value on both servers.
Also documented: on a FactorValue row the term field is now the term's
label instead of a composed sentence. GSE2018's disease factor value
reads "acute disease related to solid organ transplantation" on Gemma
1.0 and "disease related to solid organ transplantation" on Gemma 2.0.
Across 13 datasets every row that differs is a FactorValue; the
ExperimentTag and BioMaterial rows are identical on both servers.
… the usual 3 times limit
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