pinellolab/STREAM_web

STREAM_web crashes when trying to display gene on subway plot

Closed this issue · 11 comments

ggersche commented

Hi,

Thanks for this nice software. I had tried the website but as it is down, I am now trying to to use the docker image for the web interface. Sadly, it always crashes when I'm trying to display a specific gene (second step) on the subway plot.

Here is the error message I can see on the terminal :
[2019-03-24 18:36:15,508] ERROR in app: Exception on /compute/_dash-update-component [POST]
Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/flask/app.py", line 2292, in wsgi_app
response = self.full_dispatch_request()
File "/opt/conda/lib/python3.7/site-packages/flask/app.py", line 1815, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/opt/conda/lib/python3.7/site-packages/flask/app.py", line 1718, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/opt/conda/lib/python3.7/site-packages/flask/_compat.py", line 35, in reraise
raise value
File "/opt/conda/lib/python3.7/site-packages/flask/app.py", line 1813, in full_dispatch_request
rv = self.dispatch_request()
File "/opt/conda/lib/python3.7/site-packages/flask/app.py", line 1799, in dispatch_request
return self.view_functionsrule.endpoint
File "/opt/conda/lib/python3.7/site-packages/dash/dash.py", line 556, in dispatch
return self.callback_map[target_id]'callback'
File "/opt/conda/lib/python3.7/site-packages/dash/dash.py", line 513, in add_context
output_value = func(*args, **kwargs)
File "/stream_web/app.py", line 4152, in compute_trajectories
with open(gene_coords, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/RESULTS_FOLDER/STREAM_ecfb6f6c-16ec-4e21-9f5c-a2d42838a364/S5/subway_coord_Mpz.csv'

It seems to me that there is something wrong with the /tmp/RESULTS_FOLDER.
What do you think ?

Thanks for you help!

huidongchen commented

Hi,
Thanks for your interest in STREAM website. Sorry about the slow response. It has been quite hectic for a while. I was just able to get back to the issue.

You are right. It was indeed a bug in our code when we were transitioning from python2 to python3. Now it is fixed.

If you do docker pull pinellolab/stream_web, it will get updated. Please let me know how it goes.

ggersche commented
huidongchen commented

I assume the format of your cell label file is not correct. Please check the input requirement for STREAM pipeline https://github.com/pinellolab/STREAM#input-file-form

You can also find some example datasets here https://github.com/pinellolab/STREAM#example. Please make sure the files meet the required format before feeding them to STREAM.

ggersche commented
huidongchen commented

You are right ! It is optional. It is just another bug introduced by the new update.. Sorry about it. I should have tested it more carefully.

As a stopgap, can you create a label file with the same label and also a corresponding label color file? This should be able to help get around the issue. I will try to fix it shortly.

ggersche commented
huidongchen commented

Hi Gaspard,

The bugs should be fixed now if you do docker pull pinellolab/stream_web. You don't have to create a label file yourself any more.

Regarding the error message you saw, they are harmless. It's due to Dash continuously looking into a folder during the computation. The moment the folders or files are generated, the error will be gone.

Please let me know how it goes.

Best,
Huidong

ggersche commented
huidongchen commented

I'm sorry that the issue still persists. I have tested it in several different cases and they all worked. So it's a bit hard for me to debug without reproducing the error you are seeing.

But I would be more than happy to take a look if you could share with me the dataset you are using.

lucapinello commented
ggersche commented
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