Committed datatypes

[JonasIsensee]

I encountered some reproducable errors and reduced it to the following:
Committed compound datatypes that are linked like a dataset to a group cause the viewer / backend to crash:

In this reproducer, I've placed the committed type into a subgroup. Therefore the file can normally be loaded into myHDF5 web viewer and the error only occurs when trying to view the contents of /types/.

Here's the h5dump of the example file used below:

HDF5 "test.h5" {
GROUP "/" {
   DATASET "data" {
      DATATYPE  "/types/AStruct"
      DATASPACE  SIMPLE { ( 1, 1 ) / ( 1, 1 ) }
      DATA {
      (0,0): {
            1,
            2
         }
      }
   }
   GROUP "types" {
      DATATYPE "AStruct" H5T_COMPOUND {
         H5T_STD_I64LE "x";
         H5T_IEEE_F64LE "y";
      }
   }
}
}

HDF5-DIAG: Error detected in HDF5 (1.14.2) thread 0:
  #000: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5D.c line 403 in H5Dopen2(): unable to synchronously open dataset
    major: Dataset
    minor: Can't open object
  #001: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5D.c line 364 in H5D__open_api_common(): unable to open dataset
    major: Dataset
    minor: Can't open object
  #002: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5VLcallback.c line 1980 in H5VL_dataset_open(): dataset open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5VLcallback.c line 1947 in H5VL__dataset_open(): dataset open failed
    major: Virtual Object Layer
    minor: Can't open object
  #004: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5VLnative_dataset.c line 321 in H5VL__native_dataset_open(): unable to open dataset
    major: Dataset
    minor: Can't open object
  #005: /__w/libhdf5-wasm/libhdf5-wasm/build/1.14.2/_deps/hdf5-src/src/H5Dint.c line 1425 in H5D__open_name(): not a dataset
    major: Dataset
    minor: Inappropriate type


Here is some additional context:

  - User agent: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:128.0) Gecko/20100101 Firefox/128.0
  - Location: https://myhdf5.hdfgroup.org/view?url=blob%3Ahttps%3A%2F%2Fmyhdf5.hdfgroup.org%2F66f3acf9-1943-41aa-8269-a4d90b9092c3
  - File name: test.h5
  - File URL: blob:https://myhdf5.hdfgroup.org/66f3acf9-1943-41aa-8269-a4d90b9092c3
  - Service detected: Local
  - Resolved URL: blob:https://myhdf5.hdfgroup.org/66f3acf9-1943-41aa-8269-a4d90b9092c3

[axelboc]

Thanks for the report. Indeed, committed datatypes are not currently supported by h5wasm. You can reproduce also by selecting the datatypes group in the epic.h5 file in the h5wasm demo (vs in the h5grove demo).

I will use this issue to track progress:

• Investigate support – HSDS has full support; h5wasm and h5grove support visualizing/inspecting datasets with committed datatypes but not inspecting committed datatypes directly
• Support inspecting committed datatypes with h5wasm providers – adding method to read metadata for committed Datatype usnistgov/h5wasm#81 Fix parsing of committed datatype metadata with h5wasm #1708
• Support inspecting committed datatypes with h5grove provider – Support reading metadata of committed datatypes h5grove#96

Links to committed_type.h5 test file in provider demos: h5grove, h5wasm, HSDS

[bmaranville]

@JonasIsensee can you post the test.h5 file you're using here?

[JonasIsensee]

Ah, I didn't know the link in the error message blob:https://myhdf5.hdfgroup.org/.... expired so quickly.
Here's an equivalent file (as tar so that github allows me to upload it..)
committed_type.h5.tar.gz