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Add CI to read first NWB file from each dandiset #1695

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May 25, 2023
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50 changes: 50 additions & 0 deletions .github/workflows/run_dandi_read_tests.yml
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name: Run DANDI read tests
on:
schedule:
- cron: '0 6 * * *' # once per day at 1am ET
workflow_dispatch:

jobs:
run-tests:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0} # necessary for conda
steps:
- name: Cancel non-latest runs
uses: styfle/[email protected]
with:
all_but_latest: true
access_token: ${{ github.token }}

- uses: actions/checkout@v3
with:
submodules: 'recursive'
fetch-depth: 0 # tags are required for versioneer to determine the version

- name: Set up Conda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
activate-environment: ros3
environment-file: environment-ros3.yml
python-version: "3.11"
channels: conda-forge
auto-activate-base: false

- name: Install run dependencies
run: |
python -m pip install dandi pytest
python -m pip uninstall -y pynwb # uninstall pynwb
python -m pip install -e .
python -m pip list

- name: Conda reporting
run: |
conda info
conda config --show-sources
conda list --show-channel-urls

- name: Run DANDI read tests
run: |
pytest -rP tests/read_dandi/
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,7 @@

### Enhancements and minor changes
- Add testing support for Python 3.11. @rly [#1687](https://github.com/NeurodataWithoutBorders/pynwb/pull/1687)
- Add CI testing of NWB files on DANDI. @rly [#1695](https://github.com/NeurodataWithoutBorders/pynwb/pull/1695)

### Bug fixes
- Remove unused, deprecated `codecov` package from dev installation requirements. @rly
Expand Down
Empty file added tests/read_dandi/__init__.py
Empty file.
52 changes: 52 additions & 0 deletions tests/read_dandi/test_read_dandi.py
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from dandi.dandiapi import DandiAPIClient
import sys
import traceback

from pynwb import NWBHDF5IO
from pynwb.testing import TestCase


class TestReadNWBDandisets(TestCase):
"""Test reading NWB files from the DANDI Archive using ROS3."""

def test_read_first_nwb_asset(self):
"""Test reading the first NWB asset from each dandiset that uses NWB."""
client = DandiAPIClient()
dandisets = client.get_dandisets()

failed_reads = dict()
for i, dandiset in enumerate(dandisets):
dandiset_metadata = dandiset.get_raw_metadata()

# skip any dandisets that do not use NWB
if not any(
data_standard["identifier"] == "RRID:SCR_015242" # this is the RRID for NWB
for data_standard in dandiset_metadata["assetsSummary"].get("dataStandard", [])
):
continue

dandiset_identifier = dandiset_metadata["identifier"]
print("--------------")
print(f"{i}: {dandiset_identifier}")

# iterate through assets until we get an NWB file (it could be MP4)
assets = dandiset.get_assets()
first_asset = next(assets)
while first_asset.path.split(".")[-1] != "nwb":
first_asset = next(assets)
if first_asset.path.split(".")[-1] != "nwb":
print("No NWB files?!")
continue

s3_url = first_asset.get_content_url(follow_redirects=1, strip_query=True)

try:
with NWBHDF5IO(path=s3_url, load_namespaces=True, driver="ros3") as io:
io.read()
except Exception as e:
print(traceback.format_exc())
failed_reads[dandiset] = e

if failed_reads:
print(failed_reads)
sys.exit(1)