flybrainlab / flybrainlab Goto Github PK

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!

Model module needs to be redesigned.

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!

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.

Look for memory leak.

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.

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

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 :)