Committed datatypes

[axelboc]

We've just had a request in the vscode-h5web extension to support JLD2 files: silx-kit/vscode-h5web#46.

The problem is that these files make heavy use of committed datatypes — i.e. datatypes that are defined and stored as their own entities so they can potentially be referenced by multiple datasets.

Currently, h5wasm fails at reading the metadata of such datatypes. To reproduce, select the datatypes group in the epic.h5 file in H5Web's h5wasm demo (vs in the h5grove demo).

I've opened an issue in the H5Web repo to track this as well: silx-kit/h5web#1699

[bmaranville]

I can see in the source that we make no attempt to read metadata from Datatype objects at the moment, but I'm confused why there is an error in h5web when opening the datatypes group - it should just return 3 opaque Datatype objects, not try to open them as datasets, right?

[axelboc]

Indeed, likely due to a copy-pasting oversight when implementing the worker, I was calling get_dataset_metadata(fileId, path) for datatypes... https://github.com/silx-kit/h5web/blob/main/packages/h5wasm/src/worker-utils.ts#L149-L160

Commenting out the line reveals another error when trying to read attributes, on this line: https://github.com/usnistgov/h5wasm/blob/main/src/hdf5_util.cc#L226. I assume one needs to call H5Tget_create_plist when obj_type is a datatype.

[axelboc]

Contrary to what I thought, it seems that there's no problem reading the metadata of dataset that points to a committed datatype. This means that #81 will likely be sufficient to fully support committed datatypes. I'll update the issue in H5Web.

[bmaranville]

Datatype.metadata getter is in v0.7.7, just released through npm

[axelboc]

Commenting out the line reveals another error when trying to read attributes, on this line: https://github.com/usnistgov/h5wasm/blob/main/src/hdf5_util.cc#L226. I assume one needs to call H5Tget_create_plist when obj_type is a datatype.

I forgot to address this, sorry. I'll open a PR with a fix.

[bmaranville]

Can datatypes have attributes? I didn't think that was possible.

[axelboc]

I think so? https://docs.hdfgroup.org/archive/support/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/HDF5_Users_Guide/Attributes/HDF5_Attributes.htm

[bmaranville]

You're right - it mentions here the types of objects that can have attributes, and it's groups, datasets and named datatypes: https://docs.hdfgroup.org/archive/support/HDF5/doc/RM/RM_H5A.html#Annot-Iterate2