Neurovault upload using pynv

Wei_Liu · February 14, 2019, 11:52am

Hi everyone!

I am trying to create a collection and upload images to the neurovault via the pynv (https://github.com/neurolearn/pynv).

However, even though I double checked my access token (I recreated it several times even) and the pynv package, it did not work for me.

Without any error message, the new collection can be not added by the pynv. (It can be created using the website itself)

Other suggestions for uploading images are also welcomed!

Best,
Wei

SylvainTakerkart · November 29, 2019, 3:56pm

Hi!

Same problem here… I can access some basic infos (api.my_collections() works), but I cannot create a collection, upload an image or anything else… Everytime, I can the following error:

pynv.exceptions.APIError: Permission denied

Has anybody managed to upload anything to neurovault with pynv?

Cheers,

Sylvain

rwblair · December 2, 2019, 4:16pm

Do you have a link to the code being used?

I know Neuroscout uploads to NeuroVault using this code:

github.com

neuroscout/neuroscout/blob/master/neuroscout/tasks/upload.py#L118






MAP_TYPE_CHOICES = {
    't': 'T',
    'p': 'P',
    'effect': 'U',
    'variance': 'V',
}




def upload_neurovault(flask_app, file_id, n_subjects=None):
    """ Upload image file to NeuroVault
    Args:
        file_id (int): NeurovaultFileUpload object id
        n_subjects (int): Number of subjects in analysis
    """
    api = Client(access_token=flask_app.config['NEUROVAULT_ACCESS_TOKEN'])
    file_object = NeurovaultFileUpload.query.filter_by(id=file_id).one()
    basename = Path(file_object.path).parts[-1]


    contrast_name = re.findall('contrast-(.*)_', str(basename))[0]

@adelavega did you have to do anything special to get these uploads go?

adelavega · December 2, 2019, 5:05pm

The issue is that pynv available on PyPi (pip) is out of date.

To install the latest github version, try:

pip install -e git+https://github.com/neurolearn/pynv#egg=pynv

One major issue is that the neurovault address is now https, so the old version of pynv is pushing to the wrong address.

adelavega · December 2, 2019, 5:07pm

I raised an issue. https://github.com/neurolearn/pynv/issues/20

@rwblair it may be worth forking this project and keeping it up to date, seeing if they would hand over the keys, or updating the alternate project (pyneurovault) which is also out of date.