BUG streamlines URL has changed

[alessandrofelder]

Describe the bug streamlines example test fails with URL not found: Forbidden

To Reproduce

1. Run pytest -vv tests/test_examples.py --runslow --runlocal (MacOs M2 on https://github.com/brainglobe/brainrender/commit/8866e3a762476820c20cc52994e5e3a3cc21c199 with vedo 2023.4.6)
2. Output is

========================================================================================================= FAILURES ==========================================================================================================
_______________________________________________________________________________________________________ test_examples _______________________________________________________________________________________________________

    @pytest.mark.slow
    @pytest.mark.local
    def test_examples():
>       import examples

tests/test_examples.py:11: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../mambaforge/envs/brainrender-py311/lib/python3.11/site-packages/shiboken2/files.dir/shibokensupport/feature.py:139: in _import
    return original_import(name, *args, **kwargs)
examples/__init__.py:1: in <module>
    from examples import (
../../mambaforge/envs/brainrender-py311/lib/python3.11/site-packages/shiboken2/files.dir/shibokensupport/feature.py:139: in _import
    return original_import(name, *args, **kwargs)
examples/streamlines.py:19: in <module>
    streams = get_streamlines_for_region("TH")[:2]
brainrender/atlas_specific/allen_brain_atlas/streamlines.py:109: in get_streamlines_for_region
    return get_streamlines_data(
brainrender/atlas_specific/allen_brain_atlas/streamlines.py:70: in get_streamlines_data
    response = request(url)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

url = 'https://neuroinformatics.nl/HBP/allen-connectivity-viewer/json/streamlines_174957972.json.gz'

    def request(url):
        """
        Sends a request to a url
    
        :param url:
    
        """
        if not connected_to_internet():  # pragma: no cover
            raise ConnectionError(
                "No internet connection found."
            )  # pragma: no cover
    
        response = requests.get(url)
        if response.ok:
            return response
        else:  # pragma: no cover
            exception_string = "URL request failed: {}".format(
                response.reason
            )  # pragma: no cover
>       raise ValueError(exception_string)
E       ValueError: URL request failed: Forbidden

brainrender/_io.py:57: ValueError

Expected behavior Tests pass

[alessandrofelder]

@adamltyson (I think I've asked you this before - sorry) - any idea at what URL I can find the connectivity data now? Think the currently hard-coded URL is now out-of-date... presumably somewhere around https://connectivity.brain-map.org/projection/? Pointer appreciated!

[adamltyson]

This thread seems to contain the info we need to fix this.

From my understanding:

• That URL is (was) a cache of data from AIBS
• We should be able to get the data from AIBS ourselves
• If the server isn't up to it, maybe we need to cache it ourselves on GIN?

Considering the thread is 4 years old, maybe it's worth posting to see if there's a more up to date method to get this data?

[alessandrofelder]

Asked for advice on the AIBS community forum.

[alessandrofelder]

Moving this out of the https://github.com/brainglobe/brainrender/milestone/1 milestone as I had no response about the data and don't consider this issue blocking.

[adamltyson]

https://github.com/brainglobe/brainrender/pull/348 enables these "slow" tests by default. The streamlines tests are currently disabled (commented out).

[adamltyson]

This post by @fcollman illustrates how to download the data with cloud-volume. It's in a different format, and it looks like we'll need to rewrite all/most of the streamlines module.