Test pymaid 0.2.0 - Githubissues

schlegelp commented 3 years ago

Hi @jasper-tms

Since your changes are now in the master, I have also merged them into the dev branch. Can I perhaps ask you to switch to the dev branch and try it out? It's a major rework and while all tests pass, anything that pushes data to a server is tricky to test.

The most notable changes in pymaid 0.2.0 on dev are:

CatmaidNeuron and CatmaidNeuronList are now subclasses of navis.TreeNeuron and navis.NeuronList, respectively
most non-CATMAID functions (e.g. prune_by_strahler or split_axon_dendrite) have been removed and you now need to use their navis equivalent
pymaid will soon be on PyPI as python-catmaid
for consistency with navis, instances of treenode and treenode_id have been renamed to node and node_id respectively

Would be greatly appreciated!

Thanks, Philipp

jasper-tms commented 3 years ago

Yes, happy to test this out but probably not for another week or two. Will update you when I have a chance to test.

schlegelp commented 3 years ago

Have you had a chance to take it for a spin @jasper-tms? I'm considering moving forward and merging dev into the master :)

jasper-tms commented 3 years ago

Tom just 2 days ago fixed something in the catmaid API that means I can now do the uploads I want without any bugs popping up! I can get to testing pymaid 2.0 within the next few days, but please feel free to go ahead with the merge if you think it's ready and I'm happy to give feedback about what does and doesn't work for me afterward.

jasper-tms commented 3 years ago

Just ran an upload_neuron command on a small test neuron with pre- and post-synaptic connectors, treenode tags, and connector tags, and it got most of the way through the upload but not quite all the way. Treenodes, connectors, and treenode tags got uploaded but the error below happened in the Link connectors block:

~/.virtualenv/pymaid2/lib/python3.7/site-packages/pymaid/upload.py in upload_neuron(x, import_tags, import_annotations, import_connectors, reuse_existing_connectors, skeleton_id, neuron_id, force_id, source_id, source_project_id, source_url, source_type, remote_instance) 587 # Link connectors 588 links = [[resp['node_id_map'][n.node_id], 589 cn_map[n.connector_id], --> 590 rl_map[n.relation]] for n in x.connectors.itertuples()] 591 592 ln_resp = link_connector(links, remote_instance=remote_instance)

AttributeError: 'Pandas' object has no attribute 'relation'

It looks like in pymaid1, connectors had an attribute 'relation' but you changed the name of this field to be 'type' in pymaid2. Is that right? I changed n.relation to n.type and retried, and the import worked correctly.

Also looks like you changed annotations to being stored in x._annotations instead of x.annotations, but this wasn't accounted for in these two lines:

557        if import_annotations and 'annotations' in x.__dict__:
558        an = x.__dict__.get('annotations', [])

Changing both annotations to _annotations fixed this and allowed annotations to be correctly uploaded.

That's all! With those two changes, uploads work for me. Hope that helps!

schlegelp commented 3 years ago

Thanks! Pymaid 2.0.1 is now on master and has these bugs fixed. You can also get this version with pip3 install python-catmaid.

navis-org / pymaid

Test pymaid 0.2.0 #203