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getting data should be possible by just passing the dataset name in the command line and not a path to a tsv
Current Behavior
crashes
Error message
Traceback (most recent call last):
File "/home/remi/miniconda3/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3791, in get_loc
return self._engine.get_loc(casted_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "index.pyx", line 152, in pandas._libs.index.IndexEngine.get_loc
File "index.pyx", line 181, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'PortalURI'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/remi/miniconda3/bin/cohort_creator", line 8, in <module>
sys.exit(cli())
^^^^^
File "/home/remi/github/origami/cohort_creator/cohort_creator/_cli.py", line 107, in cli
get_data(
File "/home/remi/github/origami/cohort_creator/cohort_creator/main.py", line 157, in get_data
dataset_names = get_list_datasets_to_install(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/remi/github/origami/cohort_creator/cohort_creator/_utils.py", line 584, in get_list_datasets_to_install
dataset_uri = dataset_listing[dataset_listing["DatasetID"] == dataset]["PortalURI"].values[
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/home/remi/miniconda3/lib/python3.11/site-packages/pandas/core/frame.py", line 3893, in __getitem__
indexer = self.columns.get_loc(key)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/remi/miniconda3/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3798, in get_loc
raise KeyError(key) from err
KeyError: 'PortalURI'
Is there an existing issue for this?
Expected Behavior
getting data should be possible by just passing the dataset name in the command line and not a path to a tsv
Current Behavior
crashes
Error message
Environment
How to reproduce
cohort_creator install -d ds002785 -o outputs/ --dataset_types fmriprep
cohort_creator get -d ds002785 -o outputs/ --dataset_types fmriprep --datatypes func --space MNI152NLin2009cAsym -p outputs/code/participants.tsv
Anything else?
No response
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