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Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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filepath in HDF5ArraySeed's validity method be extracted with path()? #32

Open LTLA opened 3 years ago

LTLA commented 3 years ago

We're creating a Seed class that inherits from HDF5ArraySeed but overwrites path() to dynamically point to resources at different realized filepaths; a similar solution to that in #20 but for our internal datasets.

It almost works, but we need to hack around the validity method in HDF5ArraySeed so that it doesn't actually try to look up the file in @filepath (which is only guaranteed to exist when calling path(), via our internal caching mechanism).

It might be possible to use path() in the validity method, and then everything would just work off the bat.

LTLA commented 3 years ago

Also, if extensions of this nature are supported, we should stress that any methods for path() must return a normalized or path.expand()ed path. Got hit by rappdirs updates that started reporting ~ in the path and h5mread didn't like it.