Error while displaying a widget: `AttributeError: 'CaptureShell' object has no attribute 'kernel'`
rraadd88 opened this issue · comments
Hi,
When I tried to show a widget,
(1) it is displayed initially when the app is loading,
(2) but then this error is shown:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[1], line 2
1 import igv_notebook
----> 2 igv_notebook.init()
3 igv_browser= igv_notebook.Browser(
4 {
5 "genome": "hg19",
(...)
22 }
23 )
File ~/path/to/lib/python3.9/site-packages/igv_notebook/browser.py:14, in init(version)
12 def init(version = None):
13 global _igv_version
---> 14 register_filecomm()
15 register_svgcomm()
17 if version is None:
File ~/path/to/lib/python3.9/site-packages/igv_notebook/file_reader.py:61, in register_filecomm()
58 binary_file_data = read_file(path)
59 comm.send({'id': id, 'data': binary_file_data})
---> 61 get_ipython().kernel.comm_manager.register_target('file_request', target_func)
AttributeError: 'CaptureShell' object has no attribute 'kernel'
Please let me know suggestions to solve this issue.
Thanks.
Code to reproduce the error:
# installation of the widget-package
# !pip install igv-notebook #0.5.2
# app
import mercury as mr
app = mr.App(
title="igv",
show_code = False,
show_prompt=False,
)
# widget
import igv_notebook
igv_notebook.init()
igv_browser= igv_notebook.Browser(
{
"genome": "hg19",
"locus": "chr22:24,376,166-24,376,456",
"tracks": [{
"name": "BAM",
"url": "https://s3.amazonaws.com/igv.org.demo/gstt1_sample.bam",
"indexURL": "https://s3.amazonaws.com/igv.org.demo/gstt1_sample.bam.bai",
"format": "bam",
"type": "alignment"
}],
"roi": [
{
"name": "ROI set 1",
"url": "https://s3.amazonaws.com/igv.org.test/data/roi/roi_bed_1.bed",
"indexed": False,
"color": "rgba(94,255,1,0.25)"
}
]
}
)
