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MetaCell / nwb-explorer

NWB Explorer is a web application to visualise and analyse the content of NWB:N 2 files
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Error running: cannot find geppetto.vm #294

Closed CamHolman closed 1 year ago

CamHolman commented 2 years ago

Hi there,

First of all, this looks like a really useful application and I'm excited to use it. I am having an issue getting it started after following the instructions in your documentation. It seems that there is no file:

~/nwb-explorer/webapp/build/geppetto.vm

When trying to launch, I get this error and a 500: Internal Server Error when launching the notebook. Has this come up before?

I've added the output from running below and highlighted the section with the error message. The issue is also not resolved by running with docker. Any help would be greatly appreciated.

Thanks very much, Cameron

(nwb-explorer) jacobslab@dyn-209-2-235-145 nwb-explorer % ./NWBE
[W 18:36:32.162 NotebookApp] Unrecognized alias: 'library', it will have no effect. [I 18:36:32.228 NotebookApp] Authentication of /metrics is OFF, since other authentication is disabled. [W 18:36:32.553 NotebookApp] All authentication is disabled. Anyone who can connect to this server will be able to run code. [I 18:36:32.853 NotebookApp] Starting Geppetto Jupyter extension [I 18:36:32.853 NotebookApp] Using notebook notebook.ipynb [I 18:36:32.853 NotebookApp] Geppetto Jupyter extension is running! [I 18:36:32.854 NotebookApp] The port 8888 is already in use, trying another port. [I 18:36:32.855 NotebookApp] Serving notebooks from local directory: /Users/jacobslab/nwb-explorer [I 18:36:32.855 NotebookApp] Jupyter Notebook 6.4.10 is running at: [I 18:36:32.855 NotebookApp] http://localhost:8889/ [I 18:36:32.855 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [I 18:36:34.357 NotebookApp] New context path found: /. Relative routes will be added. [I 18:36:34.358 NotebookApp] Initializing library module nwb_explorer [I 18:36:36.669 NotebookApp] Adding NWBModelInterpreter [I 18:36:36.670 NotebookApp] Adding NWBDataManager [I 18:36:36.670 NotebookApp] Initializing extension silverlab [E 18:36:36.689 NotebookApp] Error evaluating extension init file nwb-extensions/silverlab/init.py Traceback (most recent call last): File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/nwb_explorer/init.py", line 42, in init_extensions eval(line) File "", line 1, in File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/utils.py", line 587, in func_call return func(pargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/pynwb/init.py", line 186, in get_class return __TYPE_MAP.get_dt_container_cls(neurodata_type, namespace) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/utils.py", line 583, in func_call return func(args[0], pargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/build/manager.py", line 523, in get_dt_container_cls self.check_dependent_types(spec, namespace) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/build/manager.py", line 546, in check_dependent_types self.get_dt_container_cls(spec.data_type_inc, namespace) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/utils.py", line 583, in func_call return func(args[0], pargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/build/manager.py", line 522, in get_dt_container_cls spec = self.__ns_catalog.get_spec(namespace, data_type) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/utils.py", line 583, in func_call return func(args[0], pargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/spec/namespace.py", line 317, in get_spec return self.__namespaces[namespace].get_spec(data_type) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/utils.py", line 583, in func_call return func(args[0], *pargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/hdmf/spec/namespace.py", line 150, in get_spec raise ValueError("No specification for '%s' in namespace '%s'" % (data_type, self.name)) ValueError: No specification for 'NWBData' in namespace 'silverlab_extended_schema' [I 18:36:36.693 NotebookApp] Adding routes starting at base path / [I 18:36:36.693 NotebookApp] Adding http route /geppettoprojects [I 18:36:36.693 NotebookApp] Complete route url: /geppettoprojects [I 18:36:36.693 NotebookApp] Adding http route /geppetto [I 18:36:36.693 NotebookApp] Complete route url: /geppetto [I 18:36:36.694 NotebookApp] Adding http route /api/image [I 18:36:36.694 NotebookApp] Complete route url: /api/image [I 18:36:36.694 NotebookApp] Adding http route /notebook [I 18:36:36.694 NotebookApp] Complete route url: /notebook [I 18:36:36.694 NotebookApp] Adding routes starting at base path / [I 18:36:36.694 NotebookApp] Adding static http route /Users/jacobslab/nwb-explorer/webapp/ pointing at [I 18:36:36.694 NotebookApp] Complete route url: /geppetto/(.) [I 18:36:36.695 NotebookApp] 302 GET /geppetto (::1) 2338.270000ms [I 18:36:36.701 NotebookApp] Calling index [I 18:36:36.702 NotebookApp] Error on Geppetto Server extension

[E 18:36:36.702 NotebookApp] Uncaught exception GET /geppetto (::1) HTTPServerRequest(protocol='http', host='localhost:8889', method='GET', uri='/geppetto', version='HTTP/1.1', remote_ip='::1') Traceback (most recent call last): File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/tornado/web.py", line 1702, in _execute result = method(*self.path_args, *self.path_kwargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/jupyter_geppetto/webapi.py", line 91, in handlerFn value = fn(self, args, **kwargs) File "/Users/jacobslab/opt/anaconda3/envs/nwb-explorer/lib/python3.7/site-packages/jupyter_geppetto/handlers.py", line 20, in index return open(PathService.get_webapp_resource(template)).read() FileNotFoundError: [Errno 2] No such file or directory: '/Users/jacobslab/nwb-explorer/webapp/build/geppetto.vm'

[E 18:36:36.740 NotebookApp] { "Host": "localhost:8889", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,image/apng,/;q=0.8,application/signed-exchange;v=b3;q=0.9", "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.102 Safari/537.36 Edg/98.0.1108.62" } [E 18:36:36.740 NotebookApp] 500 GET /geppetto (::1) 38.940000ms referer=None ^C[I 18:37:19.577 NotebookApp] interrupted Serving notebooks from local directory: /Users/jacobslab/nwb-explorer 0 active kernels Jupyter Notebook 6.4.10 is running at: http://localhost:8889/ Shutdown this notebook server (y/[n])? y [C 18:37:20.834 NotebookApp] Shutdown confirmed [I 18:37:20.835 NotebookApp] Shutting down 0 kernels [I 18:37:20.836 NotebookApp] Shutting down 0 terminals

filippomc commented 2 years ago

Hey @CamHolman thanks for the clear issue. I just tried a local installation and everything seems to be fine. The missing geppetto.vm file is probably related to an uncomplete build process. Have you run python utilities/install.py and did it finished with no errors?

Also if you only plan to use the application I suggest to give a try to http://nwbexplorer.opensourcebrain.org/ or the brand new https://v2dev.opensourcebrain.org/, which allows you to create private workspaces and use nwb explorer and other tools to work with your files.

tuanpham96 commented 1 year ago

I also had similar issue like @CamHolman when I ran it from the development branch in a conda environment. Running python utilities/install.py got 5 errors at the end.

Switching to master branch and running install.py finished with success and I could run NWBE, though the Load button was not accessible.

filippomc commented 1 year ago

Hi @tuanpham96 there was an issue in the test file generation, fixed.