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Data Table: error message when opening some single-cell datasets #398

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elapraznik opened this issue Nov 3, 2023 · 1 comment
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@elapraznik
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Describe the bug
When I pass on some loaded datasets from Single Cell Datasets widget to Data Table I get an error message. The dataset can still be opened in the data table. The datasets showcasing this error are:

  1. Healthy human bone marrow
  2. AML patient bone marrow day 0
  3. AML patient bone marrow day 15
  4. AML patient bone marrow day 31

To Reproduce
Steps to reproduce the behavior:

  1. Go to Orange canvas and open Single Cell Datasets widget
  2. Load the listed datasets
  3. Pass the loaded dataset on to Data Table

Screenshots
The error message I get in all 4 cases:

Traceback (most recent call last):
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/Orange/widgets/data/owdatasets.py", line 605, in __commit_complete
self.load_and_output(path)
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/Orange/widgets/data/owdatasets.py", line 636, in load_and_output
data = self.load_data(path)
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/orangecontrib/single_cell/widgets/owscdatasets.py", line 38, in load_data
data = Orange.data.Table(path)
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/Orange/data/table.py", line 713, in new
return cls.from_file(args[0], **kwargs)
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/Orange/data/table.py", line 1104, in from_file
data = reader.read()
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/Orange/data/io.py", line 208, in read
table = pickle.load(f)
File "/opt/miniconda3/envs/orange3/lib/python3.10/site-packages/Orange/data/variable.py", line 38, in make_variable
return cls(*args, compute_value=compute_value)
TypeError: DiscreteVariable.init() got multiple values for argument 'compute_value'

Desktop:

  • OS: macOS
  • Python Version: 3.10
  • Orange Version: 3.36.2
  • Add-on Version: Single Cell Add-on 1.5.0
@elapraznik elapraznik added the bug label Nov 3, 2023
@janezd
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janezd commented Jul 22, 2024

Apparently somebody fixed the files found by @elapraznik. When I try to read files with pure Orange (without even Qt), I still get a few errors:

  • DiscreteVariable.__init__() got multiple values for argument 'compute_value'
    • Stimulated and resting immune cells (3000 cells) from pbmc_kang2018_sample_3000.pkl.gz
  • No module named 'orangecontrib'
    • Human osteoarthritis chondrocytes from ji2019_cartilage_osteoarthritis.pkl.gz
  • PyQt4, PyQt5, PySide or PySide2 are not available for import
    • Pancreas cells in mouse from baron2016_pancreas_mouse.pkl.gz
    • Human preimplantation embryos from petropoulos2016_preimplantation_embryos.pkl.gz

I think the first two must be fixed, while the latter two are unlikely.

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