flybrainlab / flybrainlab Goto Github PK

Allow multiple workspace support in the same tab.

Installing the front end using miniconda was working just fine last week. However, now when I install it this week, I get a strange error when the install hits the nxt_gem package, see below the output provided.

Also, in my attempts to fix this, I tried updating my pip and the setuptools packages based on internet comments I saw. Didn't help.

****************************error in console ****************************

Collecting git+https://github.com/jernsting/nxt_gem.git
Cloning https://github.com/jernsting/nxt_gem.git to c:\users\saul\appdata\local\temp\pip-req-build-pwt3nfir
Running command git clone --filter=blob:none --quiet https://github.com/jernsting/nxt_gem.git 'C:\Users\saul\AppData\Local\Temp\pip-req-build-pwt3nfir'
Resolved https://github.com/jernsting/nxt_gem.git to commit 9f1ba7de35e87cb3521387cd393306a3fef5f79c
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [16 lines of output]
C:\Users\saul\miniconda3\envs\flybrainlab\lib\site-packages\setuptools_distutils\dist.py:265: UserWarning: Unknown distribution option: 'pbr'
warnings.warn(msg)
error: Multiple top-level packages discovered in a flat-layout: ['gem', 'images'].

  To avoid accidental inclusion of unwanted files or directories,
  setuptools will not proceed with this build.

  If you are trying to create a single distribution with multiple packages
  on purpose, you should not rely on automatic discovery.
  Instead, consider the following options:

  1. set up custom discovery (`find` directive with `include` or `exclude`)
  2. use a `src-layout`
  3. explicitly set `py_modules` or `packages` with a list of names

  To find more information, look for "package discovery" on setuptools docs.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.

Model module needs to be redesigned.

The run_scripts repo appears to be missing from the dev install script. It is referenced in the file, resulting in an error if nothing is done about it. Using the non-dev install script as an example, cloning the repo appears to be missing.

I'll close this if it is intentional or submit a PR if not! Thanks :)

I use the hemibrain datasets in my workspace, but when I write the query in Write Query it doesn't have any results or graphics. Then I try the code in Tutorials Part 1(b):

my_client = fbl.get_client()
res = my_client.executeNLPquery('show alpha_beta_kc')

It shows errors:

> [FBL NLP 2022-08-01 12:19:36,032] NLP successfully parsed query.
> ---------------------------------------------------------------------------
> FlyBrainLabNAserverException              Traceback (most recent call last)
> <ipython-input-19-cbe317317ce1> in <module>
> ----> 1 res = my_client.executeNLPquery('show APL')
> 
> ~/miniconda/envs/ffbo/lib/python3.7/site-packages/flybrainlab/Client.py in executeNLPquery(self, query, language, uri, queryID, returnNAOutput)
>    1465                 self.compiled = False
>    1466                 res = self.executeNAquery(
> -> 1467                     resNA, queryID=queryID, threshold=self.query_threshold
>    1468                 )
>    1469                 if 'show ' in query or 'add ' in query or 'remove ' in query:
> 
> ~/miniconda/envs/ffbo/lib/python3.7/site-packages/flybrainlab/Client.py in executeNAquery(self, task, language, uri, queryID, progressive, threshold, temp)
>    1648             self.active_na_queries.pop(queryID)
>    1649             self.NLP_result.clear_cmd()
> -> 1650             raise FlyBrainLabNAserverException(res['info']['error'])
>    1651         self.last_NAquery_result = self.active_na_queries[queryID]
>    1652         return self.active_na_queries.pop(queryID)
> 
> FlyBrainLabNAserverException: Error executing query on NeuroArch

Also,my Neu3D-1::Untitled.ipynb is black without any neurons or some visual graphics.

Thanks!

Look for memory leak.

check if you are able to pass variables by reference in TypeScript

I ran the full installation script on Ubuntu 18.04 LTS, with all the prerequisite packages in place. The installation script did not throw any error. I then ran "start.sh" to succesfully open FBL (a popup stated that the backend packages are configured correctly).

However, upon trying to connect a Neu3D widget to a dataset (I tried Hemibrain, Flycircuit, Larva and Medulla) I get the following error:

`/home/shashwat/anaconda3/envs/ffbo/lib/python3.7/site-packages/urllib3/connectionpool.py:847: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecureRequestWarning)
/home/shashwat/anaconda3/envs/ffbo/lib/python3.7/site-packages/urllib3/connectionpool.py:847: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecureRequestWarning)

ConnectionRefusedError Traceback (most recent call last)
in
13 dataset='hemibrain',
14 realm=u'realm1',
---> 15 ca_cert_file="isrgrootx1.pem",)
16 fbl.client_manager.add_client('client-Neu3D-1-fa2629de-8418-415a-bc22-912d6d02109c', _client, client_widgets=['Neu3D-1-fa2629de-8418-415a-bc22-912d6d02109c'])
17 else:

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/flybrainlab/Client.py in init(self, ssl, debug, authentication, user, secret, custom_salt, url, realm, ca_cert_file, intermediate_cert_file, FFBOLabcomm, FBLcomm, legacy, initialize_client, name, species, use_config, custom_config, widgets, dataset, log_level)
639 self.legacy = legacy
640 self.dataset = dataset
--> 641 self.init_client(ssl, user, secret, custom_salt, url, ssl_con, legacy)
642 self.findServerIDs(dataset) # Get current server IDs
643 self.connected = True

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/flybrainlab/Client.py in init_client(self, ssl, user, secret, custom_salt, url, ssl_con, legacy)
805 ) # Initialize the communication right now!
806 else:
--> 807 FBLClient.run(url=url, authmethods=[u'wampcra'], authid=user)
808
809 setProtocolOptions(FBLClient._async_session._transport,

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/autobahn_sync/core.py in run(self, url, realm, authmethods, authid, authrole, authextra, blocking, callback, **kwargs)
105 self._bootstrap(blocking, url=url, realm=realm,
106 authmethods=authmethods, authid=authid, authrole=authrole,
--> 107 authextra=authextra, **kwargs)
108 if callback:
109 callback()

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/autobahn_sync/core.py in _bootstrap(self, blocking, **kwargs)
177
178 logger.debug('[MainThread] call bootstrap')
--> 179 start_runner()
180 logger.debug('[MainThread] call decorated register/subscribe')
181 for cb in self._on_running_callbacks:

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/crochet/_eventloop.py in wrapper(function, _, args, kwargs)
508 eventual_result = run()
509 try:
--> 510 return eventual_result.wait(timeout)
511 except TimeoutError:
512 eventual_result.cancel()

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/crochet/_eventloop.py in wait(self, timeout)
239 result = self._result(timeout)
240 if isinstance(result, Failure):
--> 241 result.raiseException()
242 return result
243

~/anaconda3/envs/ffbo/lib/python3.7/site-packages/twisted/python/failure.py in raiseException(self)
473 # Python 3
474 def raiseException(self):
--> 475 raise self.value.with_traceback(self.tb)
476
477 else:

ConnectionRefusedError: Connection was refused by other side: 111: Connection refused.`

I am thus unable to use FBL with Neuroarch as intended.
Thanks!

I'm trying to follow the tutorial from the Data Loading Notebook:
https://github.com/FlyBrainLab/Tutorials/blob/master/tutorials/swc_loading_tutorial/swc_loading.ipynb
Here is the section I am looking at:

However, after running my query, even though it works, I get an error using the syntax provided:

Note I am using the Conda frontend only.

Look into floating windows using PhosphorJS, look at Golden Layout's Example.