Copy LSV text below: empty when use voila view.

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li

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Apr 18, 2021, 10:38:47 PMApr 18
to majiq_voila
Dear Paul,

I am using voila view, however, no .josn text was generated when I click the 'copy lsv' button. I would like to design RT-PCR primers by MAJIQ-SPEL.

I used the ucsc hg38 genome files which is download in ucsc.
gff file is converted from the gtf file.

command I used:
voila view /home/l/GI_DLBC/exrnaseq/results/majiq/build/splicegraph.sql /home/l/GI_DLBC/exrnaseq/results/majiq/deltapsi/

2021-04-19 10:29:10,214 (PID:113567) - INFO - Command: /home/l/miniconda3/envs/MAJIQ/bin/voila view /home/l/GI_DLBC/exrnaseq/results/majiq/build/splicegraph.sql /home/l/GI_DLBC/exrnaseq/results/majiq/deltapsi/
2021-04-19 10:29:10,215 (PID:113567) - INFO - Voila v2.0.0-05c9c32
2021-04-19 10:29:10,215 (PID:113567) - INFO - config file: /tmp/tmp1wqjjksy
2021-04-19 10:29:10,224 (PID:113567) - INFO - Using index: /home/l/GI_DLBC/exrnaseq/results/majiq/deltapsi/DLBC_NORMAL.deltapsi.voila
/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/voila/index.py:381: H5pyDeprecationWarning: dataset.value $
as been deprecated. Use dataset[()] instead.
  for row in h['index'].value:
ERROR:flask.app:Exception on /copy-lsv/ENSG00000001167:s:41079029-41079164 [POST]
Traceback (most recent call last):
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/app.py", line 2292, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/app.py", line 1815, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/app.py", line 1718, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/_compat.py", line 35, in reraise
    raise value
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/app.py", line 1813, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/app.py", line 1799, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/voila/view/deltapsi.py", line 287, in copy_lsv
    return views.copy_lsv(lsv_id, ViewDeltaPsi)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/voila/view/views.py", line 92, in copy_lsv
    with ViewSpliceGraph() as sg, view_matrix(voila_file=voila_file) as m:
TypeError: __init__() got an unexpected keyword argument 'voila_file'

Snipaste_2021-04-19_10-25-29.jpg

Paul Jewell

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Apr 27, 2021, 5:00:05 PMApr 27
to majiq_voila
Hello Li, 

I believe this was a known older bug in Voila, and the issue was patched out in newer versions. Would you be able to install the newest version from the downloads page, and try again? https://majiq.biociphers.org/app_download/

Thanks, 
-Paul

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