ARCHIVED TRAINING / hdmf-dev/hdmf

hdmf-dev__hdmf-1270

This is a preserved training example. Membership in the current training wave has not been verified.

Problem statement

[Bug]: get_data_shape on list of Data objects is incorrect
### What happened?

`get_data_shape` is used in many places, including shape validation and getting dimension labels. In NWB, an `Image` neurodata type is a descendent of `Data`, i.e., a dataset. `ImageReferences` has a field that stores a 1-D list/array of `Image` objects. However, when validating the shape of input to that field in `ImageReferences`, `get_data_shape` recurses into the `Image` data to get the shape of the images. As a result, a 1-D list of references to `Image` objects, which on disk has shape `(N, )`, will be reported by `get_data_shape` as having shape `(N, W, H)`. where (W, H) is the shape of the first image. The schema says the field should have shape `(N, )`.

Secondly, writing valid `ImageReferences` produces a warning on write:
  /Users/rly/Documents/NWB/hdmf/src/hdmf/build/objectmapper.py:874: IncorrectDatasetShapeBuildWarning: Shape of data does not match shape in spec 'ImageReferences'
    warnings.warn(msg, IncorrectDatasetShapeBuildWarning)

This occurs when getting dimension labels.

`get_data_shape` on a list/array of Data objects (a dataset of references) should return the shape of the list/array and not recurse deeper.

### Steps to Reproduce

```python
get_data_shape([Data(name="a", data=[1, 2]), Data(name="b", data=[3, 4])])
```

### Traceback

```pytb

```

### Operating System

macOS

### Python Version

3.13

### Package Versions

_No response_

Training membership

opd_e4b_cispo_v5 opd_e4b_pure_v6a opd_e4b_pure_v6b opd_e4b_pure_v7 opd_e4b_pure_v7b

Task issues extracted from preserved verified_rft_messages training examples. This is not a verified current RL wave manifest.

Task and snapshot provenance

Snapshot captured 2026-11-12T17:06:59.476467+00:00 · Autoresearch-Arena/gemma-4-developer-agent

{
  "datasets": [
    "opd_e4b_cispo_v5",
    "opd_e4b_pure_v6a",
    "opd_e4b_pure_v6b",
    "opd_e4b_pure_v7",
    "opd_e4b_pure_v7b"
  ],
  "examples": 29,
  "instance_id": "hdmf-dev__hdmf-1270",
  "problem_statement": "[Bug]: get_data_shape on list of Data objects is incorrect\n### What happened?\n\n`get_data_shape` is used in many places, including shape validation and getting dimension labels. In NWB, an `Image` neurodata type is a descendent of `Data`, i.e., a dataset. `ImageReferences` has a field that stores a 1-D list/array of `Image` objects. However, when validating the shape of input to that field in `ImageReferences`, `get_data_shape` recurses into the `Image` data to get the shape of the images. As a result, a 1-D list of references to `Image` objects, which on disk has shape `(N, )`, will be reported by `get_data_shape` as having shape `(N, W, H)`. where (W, H) is the shape of the first image. The schema says the field should have shape `(N, )`.\n\nSecondly, writing valid `ImageReferences` produces a warning on write:\n  /Users/rly/Documents/NWB/hdmf/src/hdmf/build/objectmapper.py:874: IncorrectDatasetShapeBuildWarning: Shape of data does not match shape in spec 'ImageReferences'\n    warnings.warn(msg, IncorrectDatasetShapeBuildWarning)\n\nThis occurs when getting dimension labels.\n\n`get_data_shape` on a list/array of Data objects (a dataset of references) should return the shape of the list/array and not recurse deeper.\n\n### Steps to Reproduce\n\n```python\nget_data_shape([Data(name=\"a\", data=[1, 2]), Data(name=\"b\", data=[3, 4])])\n```\n\n### Traceback\n\n```pytb\n\n```\n\n### Operating System\n\nmacOS\n\n### Python Version\n\n3.13\n\n### Package Versions\n\n_No response_",
  "repo": "hdmf-dev/hdmf",
  "source": "v2/experiments/train_data/opd_e4b_cispo_v5/verified_rft_messages.jsonl",
  "source_sha256": "a43610ad0dfb6ace95375cfae09000f41afc0338cc925af870a4ade7a9b20c4c"
}

{
  "captured_at": "2026-11-12T17:06:59.476467+00:00",
  "membership": "archived training",
  "membership_evidence": "Task issues extracted from preserved verified_rft_messages training examples. This is not a verified current RL wave manifest.",
  "name": "Preserved post-training task archive",
  "source": "Autoresearch-Arena/gemma-4-developer-agent",
  "source_revision": "016496de222aaafca0d4ee4c18efc63ba616f76e",
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