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Ensure the cell table is being written to the right path in the noteb…
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…ook test for cell clustering
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alex-l-kong committed May 27, 2022
1 parent b5cb779 commit ea212ec
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7 changes: 7 additions & 0 deletions ark/utils/notebooks_test_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -452,6 +452,13 @@ def flowsom_cell_setup(tb, flowsom_dir, pixel_dir, pixel_cluster_col='pixel_meta
# extract the parameters from the cell params JSON
tb.execute_cell('param_load')

# assert the cell table path is set accordingly
tb.inject(
"""
cell_table_path = os.path.join('%s', 'cell_table_size_normalized.csv')
""" % flowsom_dir, after='param_load'
)

# set cell_cluster_prefix
tb.inject("cell_cluster_prefix = '%s'" % cell_prefix, after='cluster_prefix')

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